Compositions and methods for detection of smn protein in a subject and treatment of a subject

ABSTRACT

Disclosed herein are compounds, compositions and methods for modulating splicing of SMN2 mRNA in a subject. Also provided are uses of disclosed compounds and compositions in the manufacture of a medicament for treatment of diseases and disorders, including spinal muscular atrophy. Also provided are kits for detecting the amount of SMN protein in a sample of cerebrospinal fluid.

SEQUENCE LISTING

The present application is being filed along with a Sequence Listing inelectronic format. The Sequence Listing is provided as a file entitledCORE0123WOSEQ_ST25.txt, created Sep. 10, 2015, which is 8 Kb in size.The information in the electronic format of the sequence listing isincorporated herein by reference in its entirety.

BACKGROUND OF THE INVENTION

Newly synthesized eukaryotic mRNA molecules, known as primarytranscripts or pre-mRNA are processed before translation. Processing ofthe pre-mRNAs includes addition of a 5′ methylated cap and anapproximately 200-250 base poly(A) tail to the 3′ end of the transcript.Processing of mRNA from pre-mRNA also frequently involves splicing ofthe pre-mRNA, which occurs in the maturation of 90-95% of mammalianmRNAs. Introns (or intervening sequences) are regions of a pre-mRNA (orthe DNA encoding it) that are not included in the coding sequence of themature mRNA. Exons are regions of a primary transcript that remain inthe mature mRNA. The exons are spliced together to form the mature mRNAsequence. Splice junctions are also referred to as splice sites with the5′ side of the junction often called the “5′ splice site,” or “splicedonor site” and the 3′ side the “3′ splice site” or “splice acceptorsite.” In splicing, the 3′ end of an upstream exon is joined to the 5′end of the downstream exon. Thus the unspliced pre-mRNA has anexon/intron junction at the 5′ end of an intron and an intron/exonjunction at the 3′ end of an intron. After the intron is removed, theexons are contiguous at what is sometimes referred to as the exon/exonjunction or boundary in the mature mRNA. Cryptic splice sites are thosewhich are less often used but may be used when the usual splice site isblocked or unavailable. Alternative splicing, defined as the splicingtogether of different combinations of exons, often results in multiplemRNA transcripts from a single gene.

Up to 50% of human genetic diseases resulting from a point mutationresult in aberrant pre-mRNA processing. Such point mutations can eitherdisrupt a current splice site or create a new splice site, resulting inmRNA transcripts comprised of a different combination of exons or withdeletions in exons. Point mutations also can result in activation of acryptic splice site or disrupt regulatory cis elements (i.e. splicingenhancers or silencers) (Cartegni et al., Nat. Rev. Genet., 2002, 3,285-298; Drawczak et al., Hum. Genet., 1992, 90, 41-54). Antisenseoligonucleotides have been used to target mutations that lead toaberrant splicing in several genetic diseases in order to redirectsplicing to give a desired splice product (Kole, Acta BiochimicaPolonica, 1997, 44, 231-238).

Antisense compounds have also been used to alter the ratio of naturallyoccurring alternate splice variants such as the long and short forms ofBcl-x pre-mRNA (U.S. Pat. No. 6,172,216; U.S. Pat. No. 6,214,986; Tayloret al., Nat. Biotechnol. 1999, 17, 1097-1100) or to force skipping ofspecific exons containing premature termination codons (Wilton et al.,Neuromuscul. Disord., 1999, 9, 330-338). U.S. Pat. No. 5,627,274 and WO94/26887 disclose compositions and methods for combating aberrantsplicing in a pre-mRNA molecule containing a mutation using antisenseoligonucleotides which do not activate RNAse H.

Proximal spinal muscular atrophy (SMA) is a genetic, neurodegenerativedisorder characterized by the loss of spinal motor neurons. SMA is anautosomal recessive disease of early onset and is currently the leadingcause of death among infants. The severity of SMA varies among patientsand has thus been classified into three types. Type I SMA is the mostsevere form with onset at birth or within 6 months and typically resultsin death within 2 years. Children with type I SMA are unable to sit orwalk. Type II SMA is the intermediate form and patients are able to sit,but cannot stand or walk. Patients with type III SMA, a chronic form ofthe disease, typically develop SMA after 18 months of age (Lefebvre etal., Hum. Mol. Genet., 1998, 7, 1531-1536).

The molecular basis of SMA is caused by the loss of both copies ofsurvival motor neuron gene 1 (SMN1), which may also be known as SMNTelomeric, a protein that is part of a multi-protein complex thought tobe involved in snRNP biogenesis and recycling. A nearly identical gene,SMN2, which may also be known as SMN Centromeric, exists in a duplicatedregion on chromosome 5q13 and modulates disease severity. Expression ofthe normal SMN1 gene results solely in expression of survival motorneuron (SMN) protein. Although SMN1 and SMN2 have the potential to codefor the same protein, SMN2 contains a translationally silent mutation atposition +6 of exon 7, which results in inefficient inclusion of exon 7in SMN2 transcripts. Thus, the predominant form of SMN2 is a truncatedversion, lacking exon 7, which is unstable and inactive (Cartegni andKrainer, Nat. Genet., 2002, 30, 377-384). Expression of the SMN2 generesults in approximately 10-20% of the SMN protein and 80-90% of theunstable/non-functional SMNdelta7 protein. SMN protein plays awell-established role in assembly of the spliceosome and may alsomediate mRNA trafficking in the axon and nerve terminus of neurons.

Antisense technology is an effective means for modulating the expressionof one or more specific gene products, including alternative spliceproducts, and is uniquely useful in a number of therapeutic, diagnostic,and research applications. The principle behind antisense technology isthat an antisense compound, which hybridizes to a target nucleic acid,modulates gene expression activities such as transcription, splicing ortranslation through one of a number of antisense mechanisms. Thesequence specificity of antisense compounds makes them extremelyattractive as tools for target validation and gene functionalization, aswell as therapeutics to selectively modulate the expression of genesinvolved in disease.

Certain antisense compounds complementary to SMN2 are known in the art.See for example, WO 2007/002390; U.S. 61/168,885; Hua et al., AmericanJ. of Human Genetics (April 2008) 82, 1-15; Singh et al., RNA Bio. 6:3,1-10 (2009). Certain antisense compounds and methods disclosed hereinposses desirable characteristics compared to such compounds and methodsknown in the art. Chimeric peptide nucleic acid molecules designed tomodulate splicing of SMN2 have been described (WO 02/38738; Cartegni andKrainer, Nat. Struct. Biol., 2003, 10, 120-125).

SUMMARY OF THE INVENTION

In certain embodiments, the present disclosure provides methodscomprising measuring the amount of SMN protein in the cerebrospinalfluid of a subject. In certain embodiments, the subject has SMA. Incertain embodiments, the method of determining the amount of SMN proteinin a biological sample, e.g. cerebrospinal fluid, comprises (a)collecting a biological sample from a subject (e.g. cerebrospinalfluid), (b) contacting the biological sample with a capture antibody,(c) contacting the biological sample with a detection antibody, and (d)measuring the amount of detection antibody in the biological sample andcalculating the amount of SMN protein in the biological sample.

In certain embodiments, the present disclosure provides methods foroptimizing the treatment of a subject having SMA comprising measuringthe amount of SMN protein in the cerebrospinal fluid of a subject andthen adjusting the subsequent frequency of dosing. In certainembodiments, the present disclosure provides methods for optimizing thetreatment of a subject having SMA comprising measuring the amount of SMNprotein in the cerebrospinal fluid of a subject and then adjustingamount of subsequent doses administered to the subject. In certainembodiments, the subject is administered ISIS 396443. In certainembodiments, the frequency of dosing of ISIS 396443 is increased. Incertain embodiments, the frequency of dosing of ISIS 396443 isdecreased. In certain embodiments, the amount of ISIS 396443administered to a patient is increased. In certain embodiments, theamount of ISIS 396443 administered to a patient is decreased. In certainembodiments, calculation of the amount of SMN protein in the biologicalsample informs a physician about the amount and frequency of subsequentdoses of ISIS 396443.

In certain embodiments, the present disclosure provides methods ofdetermining the dosing frequency of ISIS 396443 comprising:

administering a first dose of ISIS 396443 to a subject in need thereof;

detecting the amount of SMN2 protein in a sample of cerebrospinal fluidaccording to the methods described herein at the time a second dose isadministered; and

increasing or decreasing the frequency of any subsequent doses of ISIS396443.

In certain embodiments, the present disclosure provides methods ofdetermining the dosing frequency of ISIS 396443 comprising:

administering a first dose of ISIS 396443 to a subject in need thereof;

detecting the amount of SMN2 protein in a sample of cerebrospinal fluidaccording to the methods disclosed herein at the time the first dose isadministered;

detecting the amount of SMN2 protein in a sample of cerebrospinal fluidaccording to the methods disclosed herein at the time the second dose isadministered; and

increasing or decreasing the frequency of any subsequent doses of ISIS396443.

In certain embodiments, the present disclosure provides a kit fordetecting the amount of SMN protein in a sample of cerebrospinal fluidcomprising: a capture antibody labeled with a magnetic microparticle;and a detection antibody labeled with a fluorophore.

In certain embodiments, the present disclosure provides a diagnostic kitfor detecting the amount of SMN protein in a sample of cerebrospinalfluid comprising: a capture antibody labeled with a magneticmicroparticle; a detection antibody labeled with a fluorophore.

In certain embodiments, the present disclosure provides a kit fordetecting the amount of SMN protein in a sample of cerebrospinal fluidcomprising: a capture antibody labeled with a magnetic microparticleconfigured to bind with high specificity to an SMN protein; a detectionantibody labeled with a fluorophore configured to bind with highspecificity to an SMN protein; a device configured to detect thedetection antibody labeled with a fluorophore and to calculate theconcentration of SMN protein in the sample of cerebrospinal fluid.

In certain embodiments, the present disclosure provides methodscomprising administering to a subject an antisense compound comprisingan antisense oligonucleotide complementary to intron 7 of a nucleic acidencoding human SMN2 pre-mRNA, wherein the antisense compound isadministered into the cerebrospinal fluid. In certain embodiments, theadministration is into the intrathecal space. In certain embodiments,the administration is into the cerebrospinal fluid in the brain. Incertain embodiments, the administration comprises a bolus injection. Incertain embodiments, the administration comprises infusion with adelivery pump.

The present disclosure provides the following non-limiting numberedembodiments:

Embodiment 1

A method of determining the amount of SMN protein in a biological samplecomprising:

-   -   a. collecting a biological sample from a subject;    -   b. contacting the biological sample with a capture antibody;    -   c. contacting the biological sample with a detection antibody;    -   d. measuring the amount of detection antibody in the biological        sample; and calculating the amount of SMN protein in the        biological sample.

Embodiment 2

The method of embodiment 1, wherein the biological sample iscerebrospinal fluid.

Embodiment 3

The method of embodiment 1 or 2, wherein the biological sample iscontacted with the capture antibody before it is contacted with thedetection antibody.

Embodiment 4

The method of any of embodiments 1-3, comprising at least one wash step.

Embodiment 5

The method of any of embodiments 1-4, comprising at least one wash stepprior to detecting the detection antibody.

Embodiment 6

The method of any of embodiments 1-5, wherein the capture antibodyrecognizes an N-terminal epitope of the SMN2 protein.

Embodiment 7

The method of any of embodiments 1-6, wherein the capture antibodyspecifically binds to a polypeptide sequence comprising SEQ ID NO: 25.

Embodiment 8

The method of any of embodiments 1-7, wherein the capture antibodyspecifically binds to the polypeptide of SEQ ID NO: 26.

Embodiment 9

The method of any of embodiments 1-8, wherein the capture antibody islabeled with a magnetic microparticle.

Embodiment 10

The method of any of embodiments 1-9, wherein the capture antibody isMillipore antibody MABE230.

Embodiment 11

The method of any of embodiments 1-10, wherein the detection antibodyspecifically binds to the polypeptide of SEQ ID NO: 27.

Embodiment 12

The method of any of embodiments 1-11, wherein the detection antibodyspecifically binds to the polypeptide of SEQ ID NO: 28.

Embodiment 13

The method of any of embodiments 1-12, wherein the detection antibody islabeled with a fluorophore.

Embodiment 14

The method of any of embodiments 1-13, wherein the detection antibody isProteinTech antibody #60154-1-Ig.

Embodiment 15

The method of any of embodiments 1-14, wherein a salt and a surfactantare added to the sample of the cerebrospinal fluid under conditionsselected to form an assay buffer.

Embodiment 16

The method of embodiment 15, wherein the salt is NaCl.

Embodiment 17

The method of any of embodiments 15-16, wherein the salt is present in aconcentration of 100 to 1000 mM.

Embodiment 18

The method of any of embodiments 15-17, wherein the salt is present in aconcentration of 150 mM.

Embodiment 19

The method of any of embodiments 15-18, wherein the surfactant isTriton-X detergent.

Embodiment 20

The method of any of embodiments 15-19, wherein the surfactant isbetween 0.1% and 1.5% of the total volume of the assay buffer.

Embodiment 21

The method of any of embodiments 15-20, wherein the surfactant is 0.25%of the volume of the assay buffer.

Embodiment 22

The method of any of embodiments 1-21, wherein a sandwich immunoassay isused to detect the amount of SMN2 protein.

Embodiment 23

The method of any of embodiments 1-22, wherein the Singulex Erennasystem is used to detect the amount of SMN2 protein.

Embodiment 24

The method of any of embodiments 1-22, wherein an ELISA assay is used todetect the amount of SMN2 protein.

Embodiment 25

The method of any of embodiments 1-24, wherein the subject is an animal.

Embodiment 26

The method of embodiment 25, wherein the animal is a human.

Embodiment 27

The method of embodiment 25, wherein the animal is a mouse.

Embodiment 28

The method of embodiment 25, wherein the animal is a primate.

Embodiment 29

The method of any of embodiments 1-28, wherein the subject has spinalmuscular atrophy (SMA).

Embodiment 30

The method of embodiment 29, wherein the subject has type I SMA.

Embodiment 31

The method of embodiment 29, wherein the subject has type II SMA.

Embodiment 32

The method of embodiment 29, wherein the subject has type III SMA.

Embodiment 33

The method of embodiment 29, wherein the subject has type IV SMA.

Embodiment 34

The method of any of embodiments 1-33, wherein the subject has receivedat least one dose of a pharmaceutical agent for the treatment of SMA.

Embodiment 35

The method of embodiment 34, wherein the pharmaceutical agent for thetreatment of SMA is an antisense compound.

Embodiment 36

The method of embodiment 35, wherein the antisense compound isISIS396443.

Embodiment 37

The method of any of embodiments 1 to 36, wherein the amount of SMNprotein detected is between 0.1 pg/mL-10 pg/mL.

Embodiment 38

The method of any of embodiments 1 to 36, wherein the amount of SMNprotein detected is between 0.2 pg/mL-10 pg/mL.

Embodiment 39

The method of any of embodiments 1 to 36, wherein the amount of SMNprotein detected is between 0.3 pg/mL-10 pg/mL.

Embodiment 40

The method of any of embodiments 1 to 36, wherein the amount of SMNprotein detected is between 0.4 pg/mL-10 pg/mL.

Embodiment 41

The method of any of embodiments 1 to 36, wherein the amount of SMNprotein detected is between 0.5 pg/mL-10 pg/mL.

Embodiment 42

The method of any of embodiments 1 to 36, wherein the amount of SMNprotein detected is between 0.6 pg/mL-10 pg/mL.

Embodiment 43

The method of any of embodiments 1 to 36, wherein the amount of SMNprotein detected is between 0.7 pg/mL-10 pg/mL.

Embodiment 44

The method of any of embodiments 1 to 36, wherein the amount of SMNprotein detected is between 0.5 pg/mL-9 pg/mL.

Embodiment 45

The method of any of embodiments 1 to 36, wherein the amount of SMNprotein detected is between 0.5 pg/mL-8 pg/mL.

Embodiment 46

The method of any of embodiments 1 to 36, wherein the amount of SMNprotein detected is between 0.5 pg/mL-7 pg/mL.

Embodiment 47

The method of any of embodiments 1 to 36, wherein the amount of SMNprotein detected is between 0.5 pg/mL-6 pg/mL.

Embodiment 48

The method of any of embodiments 1 to 36, wherein the amount of SMNprotein detected is between 0.5 pg/mL-5 pg/mL.

Embodiment 49

The method of any of embodiments 1 to 36, wherein the amount of SMNprotein detected is less than 10 pg/mL.

Embodiment 50

The method of any of embodiments 1 to 36, wherein the amount of SMNprotein detected is less than 9 pg/mL.

Embodiment 51

The method of any of embodiments 1 to 36, wherein the amount of SMNprotein detected is less than 8 pg/mL.

Embodiment 52

The method of any of embodiments 1 to 36, wherein the amount of SMNprotein detected is less than 7 pg/mL.

Embodiment 53

The method of any of embodiments 1 to 36, wherein the amount of SMNprotein detected is less than 6 pg/mL.

Embodiment 54

The method of any of embodiments 1 to 36, wherein the amount of SMNprotein detected is less than 5 pg/mL.

Embodiment 55

The method of any of embodiments 1 to 36, wherein the amount of SMNprotein detected is less than 4 pg/mL.

Embodiment 56

The method of any of embodiments 1 to 36, wherein the amount of SMNprotein detected is less than 3 pg/mL.

Embodiment 57

The method of any of embodiments 1 to 36, wherein the amount of SMNprotein detected is less than 2 pg/mL.

Embodiment 58

The method of any of embodiments 1 to 36, wherein the amount of SMNprotein detected is less than 1.0 pg/mL.

Embodiment 59

A method of treating a subject having SMA comprising:

-   -   a. detecting the amount of SMN protein in a sample of        cerebrospinal fluid according to the method of any of        embodiments 1-58; and    -   b. administering one or more doses of ISIS 396443.

Embodiment 60

A method of determining the dosing frequency of ISIS 396443 comprising:

-   -   a. Administering a first dose of ISIS 396443 to a subject in        need thereof;    -   b. detecting the amount of SMN protein in a sample of        cerebrospinal fluid according to the method of any of        embodiments 1-58 at the time a second dose is administered; and    -   c. increasing or decreasing the frequency of any subsequent        doses of ISIS 396443.

Embodiment 61

A method of determining the dosing frequency of ISIS 396443 comprising:

-   -   a. Administering a first dose of ISIS 396443 to a subject in        need thereof;    -   b. detecting the amount of SMN protein in a sample of        cerebrospinal fluid according to the method of any of        embodiments 1-58 at the time the first dose is administered;    -   c. detecting the amount of SMN protein in a sample of        cerebrospinal fluid according to the method of any of        embodiments 1-58 at the time the second dose is administered;        and    -   d. increasing or decreasing the frequency of any subsequent        doses of ISIS 396443.

Embodiment 62

The method of embodiment 60 or 61, wherein the frequency of thesubsequent dose is increased.

Embodiment 63

The method of embodiment 60 or 61, wherein the frequency of thesubsequent dose is decreased.

Embodiment 64

The method of any of embodiments 60-63, wherein the second dose isadministered between 12 and 18 days after the first dose.

Embodiment 65

The method of any of embodiments 60-63, wherein the second dose isadministered between 24 and 34 days after the first dose.

Embodiment 66

The method of any of embodiments 60-63, wherein the second dose isadministered between 80-90 days after the first dose.

Embodiment 67

The method of any of embodiments 60-63, wherein the second dose isadministered 12-18 days after the first dose, and wherein a subsequentdose is administered 25-35 days after the first dose.

Embodiment 68

The method of any of embodiments 60-63, wherein the second dose isadministered 12-18 days after the first dose, and wherein a subsequentdose is administered 80-90 days after the first dose.

Embodiment 69

The method of any of embodiments 60-63, wherein the second dose isadministered 25-35 days after the first dose, a third dose isadministered 80-90 days after the first dose, and a fourth dose isadministered 270-280 days after the first dose.

Embodiment 70

The method of any of embodiments 60-63, wherein the second dose isadministered 25-35 days after the first dose, a third dose isadministered 80-90 days after the first dose, a fourth dose isadministered 270-280 days after the first dose, and each subsequent dosethereafter is administered at six month intervals.

Embodiment 71

The method of any of embodiments 60-63, wherein the second dose isadministered 12-18 days after the first dose, a third dose isadministered 25-35 days after the first dose, a fourth dose isadministered 60-70 days after the first dose, a fifth dose isadministered 178-188 days after the first dose, and a sixth dose isadministered 298-308 days after the first dose is administered.

Embodiment 72

The method of any of embodiments 59-71, wherein the amount of SMNprotein detected at the time the second dose is administered is 50%greater than the amount of SMN protein detected at the time the firstdose was administered.

Embodiment 73

The method of any of embodiments 59-71, wherein the amount of SMNprotein detected at the time the second dose is administered is 60%greater than the amount of SMN protein detected at the time the firstdose was administered.

Embodiment 74

The method of any of embodiments 59-71, wherein the amount of SMNprotein detected at the time the second dose is administered is 70%greater than the amount of SMN protein detected at the time the firstdose was administered.

Embodiment 75

The method of any of embodiments 59-71, wherein the amount of SMNprotein detected at the time the second dose is administered is 80%greater than the amount of SMN protein detected at the time the firstdose was administered.

Embodiment 76

The method of any of embodiments 59-71, wherein the amount of SMNprotein detected at the time the second dose is administered is 90%greater than the amount of SMN protein detected at the time the firstdose was administered.

Embodiment 77

The method of any of embodiments 59-71, wherein the amount of SMNprotein detected at the time the second dose is administered is 100%greater than the amount of SMN protein detected at the time the firstdose was administered.

Embodiment 78

The method of any of embodiments 59-71, wherein the amount of SMNprotein detected at the time the second dose is administered is at least100% greater than the amount of SMN protein detected at the time thefirst dose was administered.

Embodiment 79

The method of any of embodiments 59-71, wherein the amount of SMNprotein detected at the time the second dose is administered is at least110% greater than the amount of SMN protein detected at the time thefirst dose was administered.

Embodiment 80

The method of any of embodiments 59-71, wherein the amount of SMNprotein detected at the time the second dose is administered is at least120% greater than the amount of SMN protein detected at the time thefirst dose was administered.

Embodiment 81

The method of any of embodiments 59-71, wherein the amount of SMNprotein detected at the time the second dose is administered is at least150% greater than the amount of SMN protein detected at the time thefirst dose was administered.

Embodiment 82

The method of any of embodiments 59-71, wherein the amount of SMNprotein detected at the time the second dose is administered is at least200% greater than the amount of SMN protein detected at the time thefirst dose was administered.

Embodiment 83

The method of any of embodiments 59-71, wherein the dose is about 1milligram.

Embodiment 84

The method of any of embodiments 59-71, wherein the dose is about 2milligrams.

Embodiment 85

The method of any of embodiments 59-71, wherein the dose is about 3milligrams.

Embodiment 86

The method of any of embodiments 59-71, wherein the dose is about 4milligrams.

Embodiment 87

The method of any of embodiments 59-71, wherein the dose is about 5milligrams.

Embodiment 88

The method of any of embodiments 59-71, wherein the dose is about 6milligrams.

Embodiment 89

The method of any of embodiments 59-71, wherein the dose is about 7milligrams.

Embodiment 90

The method of any of embodiments 59-71, wherein the dose is about 8milligrams.

Embodiment 91

The method of any of embodiments 59-71, wherein the dose is about 9milligrams.

Embodiment 92

The method of any of embodiments 59-71, wherein the dose is about 10milligrams.

Embodiment 93

The method of any of embodiments 59-71, wherein the dose is about 11milligrams.

Embodiment 94

The method of any of embodiments 59-71, wherein the dose is about 12milligrams.

Embodiment 95

The method of any of embodiments 59-71, wherein the dose is about 13milligrams.

Embodiment 96

The method of any of embodiments 59-71, wherein the dose is about 14milligrams.

Embodiment 97

The method of any of embodiments 59-71, wherein the dose is about 15milligrams.

Embodiment 98

The method of any of embodiments 59-71, wherein the dose is less than 20milligrams.

Embodiment 99

The method of any of embodiments 59-71, wherein the dose is less than 15milligrams.

Embodiment 100

The method of any of embodiments 59-71, wherein the dose is less than 10milligrams.

Embodiment 101

The method of any of embodiments 59-71, wherein the dose is less than 5milligrams.

Embodiment 102

The method of any of embodiments 59-71, wherein the dose is about 4.8milligrams.

Embodiment 103

The method of any of embodiments 59-71, wherein the dose is about 5.16milligrams.

Embodiment 104

The method of any of embodiments 59-71, wherein the dose is about 5.4milligrams.

Embodiment 105

The method of any of embodiments 59-71, wherein the dose is about 7.2milligrams.

Embodiment 106

The method of any of embodiments 59-71, wherein the dose is about 7.74milligrams.

Embodiment 107

The method of any of embodiments 59-71, wherein the dose is about 8.10milligrams.

Embodiment 108

The method of any of embodiments 59-71, wherein the dose is about 9.60milligrams.

Embodiment 109

The method of any of embodiments 59-71, wherein the dose is about 10.32milligrams.

Embodiment 110

The method of any of embodiments 59-71, wherein the dose is about 10.80milligrams.

Embodiment 111

The method of any of embodiments 59-71, wherein the dose is about 11.3milligrams.

Embodiment 112

The method of any of embodiments 59-71, wherein the dose is about 12.88milligrams.

Embodiment 113

The method of any of embodiments 59-71, wherein the dose is about 13.5milligrams.

Embodiment 114

The method of any of embodiments 59-71, wherein the dose is about 14.13milligrams.

Embodiment 115

The method of any of embodiments 59-71, wherein the dose is about 12.9milligrams.

Embodiment 116

The method of any of embodiments 59-71, wherein the dose is about 13.5milligrams.

Embodiment 117

The method of any of embodiments 59-71, wherein the dose is about 14.4milligrams.

Embodiment 118

The method of any of embodiments 59-71, wherein the dose is about 15.5milligrams.

Embodiment 119

The method of any of embodiments 59-71, wherein the dose is about 16.2milligrams.

Embodiment 120

The method of any of embodiments 59-71, wherein the dose is about 17.0milligrams.

Embodiment 121

The method of any of embodiments 59-71, wherein the dose is about 16milligrams.

Embodiment 122

The method of any of embodiments 59-71, wherein the dose is about 18milligrams.

Embodiment 123

The method of any of embodiments 1-22, wherein the dose is an equivalentdose.

Embodiment 124

The method of any of embodiments 1-22, wherein the dose is an adjusteddose.

Embodiment 125

The method of embodiment 124, wherein the adjusted dose is determined byCSF volume scaling.

Embodiment 126

A kit for detecting the amount of SMN protein in a sample ofcerebrospinal fluid comprising:

-   -   a. a capture antibody labeled with a magnetic microparticle;    -   b. a detection antibody labeled with a fluorophore.

Embodiment 127

A diagnostic kit for detecting the amount of SMN protein in a sample ofcerebrospinal fluid comprising:

-   -   a. a capture antibody labeled with a magnetic microparticle;    -   b. a detection antibody labeled with a fluorophore.

Embodiment 128

A kit for detecting the amount of SMN protein in a sample ofcerebrospinal fluid comprising:

-   -   a. a capture antibody labeled with a magnetic microparticle        configured to bind with high specificity to an SMN protein;    -   b. a detection antibody labeled with a fluorophore configured to        bind with high specificity to an SMN protein;    -   c. a device configured to detect the detection antibody labeled        with a fluorophore and to calculate the concentration of SMN        protein in the sample of cerebrospinal fluid.

Embodiment 129

The kit of any of embodiments 126-128, wherein the capture antibody isMillipore antibody MABE230.

Embodiment 130

The kit of any of embodiments 126-129, wherein the detection antibody isProteinTech antibody #60154-1-Ig.

DETAILED DESCRIPTION OF THE INVENTION

It is to be understood that both the foregoing general description andthe following detailed description are exemplary and explanatory onlyand are not restrictive of the invention, as claimed. Herein, the use ofthe singular includes the plural unless specifically stated otherwise.As used herein, the use of“or” means “and/or” unless stated otherwise.Furthermore, the use of the term “including” as well as other forms,such as “includes” and “included”, is not limiting. Also, terms such as“element” or “component” encompass both elements and componentscomprising one unit and elements and components that comprise more thanone subunit, unless specifically stated otherwise.

The section headings used herein are for organizational purposes onlyand are not to be construed as limiting the subject matter described.All documents, or portions of documents, cited in this application,including, but not limited to, patents, patent applications, articles,books, and treatises, are hereby expressly incorporated by reference intheir entirety for any purpose.

I. Definitions

Unless specific definitions are provided, the nomenclature utilized inconnection with, and the procedures and techniques of, analyticalchemistry, synthetic organic chemistry, and medicinal and pharmaceuticalchemistry described herein are those well known and commonly used in theart. Standard techniques may be used for chemical synthesis, andchemical analysis. Certain such techniques and procedures may be foundfor example in “Carbohydrate Modifications in Antisense Research” Editedby Sangvi and Cook, American Chemical Society, Washington D.C., 1994;“Remington's Pharmaceutical Sciences,” Mack Publishing Co., Easton, Pa.,18th edition, 1990; and “Antisense Drug Technology, Principles,Strategies, and Applications” Edited by Stanley T. Crooke, CRC Press,Boca Raton, Fla.; and Sambrook et al., “Molecular Cloning, A laboratoryManual,” 2^(nd) Edition, Cold Spring Harbor Laboratory Press, 1989,which are hereby incorporated by reference for any purpose. Wherepermitted, all patents, applications, published applications and otherpublications and other data referred to throughout in the disclosureherein are incorporated by reference in their entirety.

Unless otherwise indicated, the following terms have the followingmeanings:

“Nucleoside” means a compound comprising a heterocyclic base moiety anda sugar moiety. Nucleosides include, but are not limited to, naturallyoccurring nucleosides, modified nucleosides, and nucleosides havingmimetic bases and/or sugar groups. Nucleosides may be modified with anyof a variety of substituents.

“Sugar moiety” means a natural or modified sugar or sugar surrogate.

“Natural sugar” means a ribofuranose moiety of DNA (2′-H) or RNA(2′-OH).

“Modified sugar” means a ribofuranose moiety comprising at least onesubstituent other than that of a natural sugar.

“Sugar surrogate” means a structure other than a ribofuranose ring whichis capable of substituting for the sugar of a nucleoside. Examples ofsugar surrogates include, but are not limited to, open ring systems,6-membered rings, sugars in which the oxygen is replace with, forexample, sulfur or nitrogen. For example, sugar surrogates include, butare not limited to morpholinos and 4′-thio-containing sugars.

“Nucleobase” means the heterocyclic base portion of a nucleoside.Nucleobases may be naturally occurring or may be modified. In certainembodiments, a nucleobase may comprise any atom or group of atomscapable of hydrogen bonding to a nucleobase of another nucleic acid.

“Nucleotide” means a nucleoside comprising a phosphate linking group. Asused herein, nucleosides include nucleotides.

“Modified nucleoside” a nucleoside comprising at least one modificationcompared to naturally occurring RNA or DNA nucleosides. Suchmodification may be at the sugar moiety and/or at the nucleobase.

“Bicyclic nucleoside” or “BNA” means a nucleoside wherein the sugarmoiety of the nucleoside comprises a bridge connecting two carbon atomsof the sugar ring, thereby forming a bicyclic sugar moiety.

“4′-2′ bicyclic nucleoside” means a bicyclic nucleoside comprising afuranose ring comprising a bridge connecting two carbon atoms of thefuranose ring connects the 2′ carbon atom and the 4′ carbon atom of thesugar ring.

“2′-modified” or “2′-substituted” means a nucleoside comprising a sugarcomprising a substituent at the 2′ position other than H or OH.

“2′-OMe” or “2′-OCH₃” or “2′-O-methyl” each means a nucleosidecomprising a sugar comprising an —OCH₃ group at the 2′ position of thesugar ring.

“MOE” or “2′-MOE” or “2′-OCH₂CH₂OCH₃” or “2′-O-methoxyethyl” each meansa nucleoside comprising a sugar comprising a —OCH₂CH₂OCH₃ group at the2′ position of the sugar ring.

“Oligonucleotide” means a compound comprising a plurality of linkednucleosides. In certain embodiments, one or more of the plurality ofnucleosides is modified. In certain embodiments, an oligonucleotidecomprises one or more ribonucleosides (RNA) and/or deoxyribonucleosides(DNA).

“Oligonucleoside” means an oligonucleotide in which none of theinternucleoside linkages contains a phosphorus atom. As used herein,oligonucleotides include oligonucleosides.

“Modified oligonucleotide” means an oligonucleotide comprising at leastone modified nucleoside and/or at least one modified internucleosidelinkage.

“Internucleoside linkage” means a covalent linkage between adjacentnucleosides of an oligonucleotide.

“Naturally occurring internucleoside linkage” means a 3′ to 5′phosphodiester linkage.

“Modified internucleoside linkage” means any internucleoside linkageother than a naturally occurring internucleoside linkage.

“Oligomeric compound” means a compound comprising an oligonucleotide. Incertain embodiments, an oligomeric compound consists of anoligonucleotide. In certain embodiments, an oligomeric compound furthercomprises one or more conjugate and/or terminal groups.

“Antisense compound” means an oligomeric compound, at least a portion ofwhich is at least partially complementary to a target nucleic acid towhich it hybridizes, wherein such hybridization results at least oneantisense activity.

“Antisense oligonucleotide” means an antisense compound wherein theoligomeric compound consists of an oligonucleotide.

“Antisense activity” refers to any detectable and/or measurable effectattributable to the hybridization of an antisense compound to its targetnucleic acid. In certain embodiments, such antisense activity is anincrease or decrease in an amount of a nucleic acid or protein. Incertain embodiments, such antisense activity is a change in the ratio ofsplice variants of a nucleic acid or protein. In certain embodiments,such antisense activity is a phenotypic change in a cell and/or subject.

“Detecting” or “measuring” of antisense activity may be direct orindirect. For example, in certain embodiments, antisense activity isassessed by detecting and/or measuring the amount of target nucleic acidor protein or the relative amounts of splice variants of a targetnucleic acid or protein. In certain embodiments, antisense activity isdetected by observing a phenotypic change in a cell or animal. Inconnection with any activity, response, or effect, the terms “detecting”and “measuring,” indicate that a test for detecting or measuring isperformed. Such detection and/or measuring may include values of zero.Thus, if a test for detection or measuring results in a finding of noactivity (activity of zero), the step of detecting or measuring theactivity has nevertheless been performed.

“Target nucleic acid” refers to any nucleic acid molecule theexpression, amount, or activity of which is capable of being modulatedby an antisense compound.

“Target mRNA” means a pre-selected RNA molecule that encodes a protein.

“Target pre-mRNA” means a pre-selected RNA transcript that has not beenfully processed into mRNA. Notably, pre-mRNA includes one or moreintron.

“Target protein” means a protein encoded by a target nucleic acid.

“Modulation” means to a perturbation of function or activity. In certainembodiments, modulation means an increase in gene expression. In certainembodiments, modulation means a decrease in gene expression.

“Expression” means any functions and steps by which a gene's codedinformation is converted into structures present and operating in acell.

“Nucleobase sequence” means the order of contiguous nucleobases, in a 5′to 3′ orientation, independent of any sugar, linkage, and/or nucleobasemodification.

“Contiguous nucleobases” means nucleobases immediately adjacent to eachother in a nucleic acid.

“Nucleobase complementarity” means the ability of two nucleobases topair non-covalently via hydrogen bonding.

“Complementary” means that a first nucleic acid is capable ofhybridizing to a second nucleic acid under stringent hybridizationconditions. For example, an antisense compound is complementary to itstarget nucleic acid if it is capable of hybridizing to the targetnucleic acid under stringent hybridization conditions.

“Fully complementary” means each nucleobase of a first nucleic acid iscapable of pairing with a nucleobase at each corresponding contiguousposition in a second nucleic acid.

“Percent complementarity” of an antisense compound means the percentageof nucleobases of the antisense compound that are complementary to anequal-length portion of a target nucleic acid. Percent complementarityis calculated by dividing the number of nucleobases of the antisenseoligonucleotide that are complementary to nucleobases at correspondingcontiguous positions in the target nucleic acid by the total length ofthe antisense compound.

“Percent identity” means the number of nucleobases in first nucleic acidthat are identical to nucleobases at corresponding positions in a secondnucleic acid, divided by the total number of nucleobases in the firstnucleic acid.

“Hybridize” means the annealing of complementary nucleic acids thatoccurs through nucleobase complementarity.

“Mismatch” means a nucleobase of a first nucleic acid that is notcapable of pairing with a nucleobase at a corresponding position of asecond nucleic acid.

“Identical nucleobase sequence” means having the same nucleobasesequence, independent of any chemical modifications to the nucleosides.

“Different modifications” or “differently modified” refer to nucleosidesor internucleoside linkages that have different nucleoside modificationsor internucleoside linkages than one another, including absence ofmodifications. Thus, for example, a MOE nucleoside and an unmodified DNAnucleoside are “differently modified,” even though the DNA nucleoside isunmodified. Likewise, DNA and RNA are “differently modified,” eventhough both are naturally-occurring unmodified nucleosides. Nucleosidesthat are the same but for comprising different nucleobases are notdifferently modified, unless otherwise indicated. For example, anucleoside comprising a 2′-OMe modified sugar and an adenine nucleobaseand a nucleoside comprising a 2′-OMe modified sugar and a thyminenucleobase are not differently modified.

“The same modifications” refer to nucleosides and internucleosidelinkages (including unmodified nucleosides and internucleoside linkages)that are the same as one another. Thus, for example, two unmodified DNAnucleoside have “the same modification,” even though the DNA nucleosideis unmodified.

“Type of modification” or nucleoside of a “type” means the modificationof a nucleoside and includes modified and unmodified nucleosides.Accordingly, unless otherwise indicated, a “nucleoside having amodification of a first type” may be an unmodified nucleoside.

“Separate regions” of an oligonucleotide means a portion of anoligonucleotide wherein the nucleosides and internucleoside linkageswithin the region all comprise the same modifications; and

the nucleosides and/or the internucleoside linkages of any neighboringportions include at least one different modification.

“Motif” means a pattern of modified and/or unmodified nucleobases,sugars, and/or internucleoside linkages in an oligonucleotide.

“Fully modified oligonucleotide” means each nucleobase, each sugar,and/or each internucleoside linkage is modified.

“Uniformly modified oligonucleotide” means each nucleobase, each sugar,and/or each internucleoside linkage has the same modification throughoutthe modified oligonucleotide.

“Alternating motif” means an oligonucleotide or a portion thereof,having at least four separate regions of modified nucleosides in apattern (AB)_(n)A_(m) where A represents a region of nucleosides havinga first type of modification; B represent a region of nucleosides havinga different type of modification; n is 2-15; and m is 0 or 1. Thus, incertain embodiments, alternating motifs include 4, 5, 6, 7, 8, 9, 10,11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 or more alternating regions.In certain embodiments, each A region and each B region independentlycomprises 1-4 nucleosides.

“Subject” means a human or non-human animal selected for treatment ortherapy.

“Subject in need thereof” means a subject identified as in need of atherapy or treatment. In such embodiments, a subject has one or moreindications of having or developing SMA.

“Administering” means providing a pharmaceutical agent or composition toa subject, and includes, but is not limited to, administering by amedical professional and self-administering.

“Parenteral administration,” means administration through injection orinfusion. Parenteral administration includes, but is not limited to,subcutaneous administration, intravenous administration, orintramuscular administration.

“Systemic administration” means administration to an area other than theintended locus of activity. Examples or systemic administration aresubcutaneous administration and intravenous administration, andintraperitoneal administration.

“Subcutaneous administration” means administration just below the skin.

“Intravenous administration” means administration into a vein.

“Cerebrospinal fluid” or “CSF” means the fluid filling the space aroundthe brain and spinal cord.

“Administration into the cerebrospinal fluid” means any administrationthat delivers a substance directly into the CSF.

“Intracerebroventricular” or “ICV” mean administration into theventricular system of the brain.

“Intrathecal” or “IT” means administration into the CSF under thearachnoid membrane which covers the brain and spinal cord. IT injectionis performed through the theca of the spinal cord into the subarachnoidspace, where a pharmaceutical agent is injected into the sheathsurrounding the spinal cord.

“Induction phase” means a dosing phase during which administration isinitiated and steady state concentrations of active pharmaceutical agentare achieved in a target tissue. For example, an induction phase is adosing phase during which steady state concentrations of antisenseoligonucleotide are achieved in liver.

“Maintenance phase” means a dosing phase after target tissue steadystate concentrations of drug have been achieved.

“Duration” means the period of time during which an activity or eventcontinues. For example, the duration of an induction phase is the periodof time during which induction doses are administered.

“Maintenance dose” means a dose administered at a single administrationduring the maintenance phase. As used herein, “induction dose” means adose administered at a single administration during the induction phase.

“Co-administration” means administration of two or more pharmaceuticalagents to a subject. The two or more pharmaceutical agents may be in asingle pharmaceutical composition, or may be in separate pharmaceuticalcompositions. Each of the two or more pharmaceutical agents may beadministered through the same or different routes of administration.Co-administration encompasses administration in parallel orsequentially.

“Therapy” means a disease treatment method. In certain embodiments,therapy includes, but is not limited to surgical therapies, chemicaltherapies, and physical interventions, such as assisted respiration,feeding tubes, and physical therapy for the purpose of increasingstrength.

“Treatment” means the application of one or more specific proceduresused for the cure or amelioration of a disease. In certain embodiments,the specific procedure is the administration of one or morepharmaceutical agents.

“Amelioration” means a lessening of severity of at least one indicatorof a condition or disease. In certain embodiments, amelioration includesa delay or slowing in the progression of one or more indicators of acondition or disease. The severity of indicators may be determined bysubjective or objective measures which are known to those skilled in theart.

“Prevent the onset of” means to prevent the development a condition ordisease in a subject who is at risk for developing the disease orcondition. In certain embodiments, a subject at risk for developing thedisease or condition receives treatment similar to the treatmentreceived by a subject who already has the disease or condition.

“Delay the onset of” means to delay the development of a condition ordisease in a subject who is at risk for developing the disease orcondition.

“Slow the progression of” means that the severity of at least onesymptom associated with a disease or condition worsens less quickly.

“Exon 7 amino acids” means the portion of an SMN protein that correspondto exon 7 of the SMN RNA. Exon 7 amino acids are present in SMN proteinexpressed from SMN RNA where exon 7 was not excluded during splicing.

“SMN protein” means normal full length survival motor neuron protein.SMN may be expressed from either an SMN1 gene or from an SMN2 gene,provided that exon 7 is present in the mature mRNA and the exon 7 aminoacids are present in the SMN protein.

“Dose” means a specified quantity of a pharmaceutical agent provided ina single administration or over a specified amount of time. In certainembodiments, a dose may be administered in two or more boluses, tablets,or injections. For example, in certain embodiments, where subcutaneousor intrathecal or ICV administration is desired, the desired doserequires a volume not easily accommodated by a single injection. In suchembodiments, two or more injections may be used to achieve the desireddose. In the setting of continuous infusion, dose may be expressed asthe quantity of a pharmaceutical agent delivered per unit of time.

“Dosage unit” means a form in which a pharmaceutical agent is provided.In certain embodiments, a dosage unit is a vial containing lyophilizedoligonucleotide. In certain embodiments, a dosage unit is a vialcontaining reconstituted oligonucleotide.

“Equivalent dose” means a dose amount that is used to calculate anadjusted dose, wherein the adjusted dose is based on the CSF volume,dose concentration, or any other criteria known to one having skill inthe art. For example, in certain embodiments it may be desirable toadminister an equivalent dose of 12 mg of ISIS 396443 to a patienthaving one or more symptoms of SMA, however based on the patient's ageand estimated CSF volume the actual dose of ISIS 396443 may be adjustedto an amount less than 12 mg. For example, it may be desirable toadminister an equivalent dose of 12 mg of ISIS 396443 to an SMA patientbetween 0 and 3 months of age, however based on the patient's age andestimated CSF volume, the actual adjusted dose of ISIS 396443 receivedby the SMA patient would be 9.6 mg. In certain embodiments, adjusteddoses may be calculated based on a desired equivalent dose by using CSFvolume scaling as described in Matsuzawa J, Matsui M, Konishi T, NoguchiK, Gur R C, Bilker W, Miyawaki T. Age-related volumetric changes ofbrain gray and white matter in healthy infants and children. CerebCortex 2001 April; 11(4):335-342, which is hereby incorporated byreference in its entirety).

“Adjusted dose” means a dose that is adjusted from a dose or equivalentdose. In certain embodiments and adjusted dose is based on one or morecriteria known to those having skill in the art. In certain embodimentsthe adjusted dose is based on the patient's age, weight, or estimatedCSF volume. In certain embodiments, an adjusted dose is derived from anequivalent dose. In certain embodiments, adjusted doses may becalculated based on a desired equivalent dose by using CSF volumescaling as described in Matsuzawa J, Matsui M, Konishi T, Noguchi K, GurR C, Bilker W, Miyawaki T. Age-related volumetric changes of brain grayand white matter in healthy infants and children. Cereb Cortex 2001April; 11(4):335-342, which is hereby incorporated by reference in itsentirety).

“Therapeutically effective amount” means an amount of a pharmaceuticalagent that provides a therapeutic benefit to an animal.

“Pharmaceutical composition” means a mixture of substances suitable foradministering to an individual that includes a pharmaceutical agent. Forexample, a pharmaceutical composition may comprise a modifiedoligonucleotide and a sterile aqueous solution.

“Acceptable safety profile” means a pattern of side effects that iswithin clinically acceptable limits.

“Side effect” means a physiological response attributable to a treatmentother than desired effects.

1. Certain Modified Oligonucleotides

In certain embodiments, the present invention provides methods andcompositions involving antisense oligonucleotides comprising one or moremodification compared to oligonucleotides of naturally occurringoligomers, such as DNA or RNA. Such modified antisense oligonucleotidesmay possess one or more desirable properties. Certain such modificationsalter the antisense activity of the antisense oligonucleotide, forexample by increasing affinity of the antisense oligonucleotide for itstarget nucleic acid, increasing its resistance to one or more nucleases,and/or altering the pharmacokinetics or tissue distribution of theoligonucleotide. In certain embodiments, such modified antisenseoligonucleotides comprise one or more modified nucleosides and/or one ormore modified nucleoside linkages and/or one or more conjugate groups.

a. Certain Modified Nucleosides

In certain embodiments, antisense oligonucleotides comprise one or moremodified nucleosides. Such modified nucleosides may include a modifiedsugar and/or a modified nucleobase. In certain embodiments,incorporation of such modified nucleosides in an oligonucleotide resultsin increased affinity for a target nucleic acid and/or increasedstability, including but not limited to, increased resistance tonuclease degradation, and or improved toxicity and/or uptake propertiesof the modified oligonucleotide.

i. Certain Nucleobases

The naturally occurring base portion of nucleosides are heterocyclicbase, typically purines and pyrimidines. In addition to “unmodified” or“natural” nucleobases such as the purine nucleobases adenine (A) andguanine (G), and the pyrimidine nucleobases thymine (T), cytosine (C)and uracil (U), many modified nucleobases or nucleobase mimetics knownto those skilled in the art are amenable to incorporation into thecompounds described herein. In certain embodiments, a modifiednucleobase is a nucleobase that is fairly similar in structure to theparent nucleobase, such as for example a 7-deaza purine, a 5-methylcytosine, or a G-clamp. In certain embodiments, nucleobase mimeticinclude more complicated structures, such as for example a tricyclicphenoxazine nucleobase mimetic. Methods for preparation of the abovenoted modified nucleobases are well known to those skilled in the art.

ii. Certain Modified Sugars and Sugar Surrogates

Antisense oligonucleotides of the present invention can optionallycontain one or more nucleosides wherein the sugar moiety is modified,compared to a natural sugar. Oligonucleotides comprising such sugarmodified nucleosides may have enhanced nuclease stability, increasedbinding affinity or some other beneficial biological property. Suchmodifications include without limitation, addition of substituentgroups, bridging of non-geminal ring atoms to form a bicyclic nucleicacid (BNA), replacement of the ribosyl ring oxygen atom with S, N(R), orC(R₁)(R)₂ (R=H, C₁-C₁₂ alkyl or a protecting group) and combinations ofthese such as for example a 2′-F-5′-methyl substituted nucleoside (seePCT International Application WO 2008/101157 Published on Aug. 21, 2008for other disclosed 5′,2′-bis substituted nucleosides) or replacement ofthe ribosyl ring oxygen atom with S with further substitution at the2′-position (see published U.S. Patent Application US2005-0130923,published on Jun. 16, 2005) or alternatively 5′-substitution of a BNA(see PCT International Application WO 2007/134181 Published on Nov. 22,2007 wherein LNA is substituted with for example a 5′-methyl or a5′-vinyl group).

Examples of nucleosides having modified sugar moieties include withoutlimitation nucleosides comprising 5′-vinyl, 5′-methyl (R or S), 4′-S,2′-F, 2′-OCH₃ and 2′-O(CH₂)₂OCH₃ substituent groups. The substituent atthe 2′ position can also be selected from allyl, amino, azido, thio,O-allyl, O—C₁-C₁₀ alkyl, OCF₃, O(CH₂)₂SCH₃, O(CH₂)₂—O—N(R_(m))(R_(n)),and O—CH₂—C(═O)—N(R_(m))(R_(n)), where each R_(m) and R_(n) is,independently, H or substituted or unsubstituted C₁-C₁₀ alkyl.

Examples of bicyclic nucleic acids (BNAs) include without limitationnucleosides comprising a bridge between the 4′ and the 2′ ribosyl ringatoms. In certain embodiments, antisense compounds provided hereininclude one or more BNA nucleosides wherein the bridge comprises one ofthe formulas: 4′-β-D-(CH₂)—O-2′ (β-D-LNA); 4′-(CH₂)—S-2′;4′-α-L-(CH₂)—O-2′ (α-L-LNA); 4′-(CH₂)₂—O-2′ (ENA); 4′-C(CH₃)₂—O-2′ (seePCT/US2008/068922); 4′-CH(CH₃)—O-2′ and 4′-C—H(CH₂OCH₃)—O-2′ (see U.S.Pat. No. 7,399,845, issued on Jul. 15, 2008); 4′-CH₂—N(OCH₃)-2′ (seePCT/US2008/064591); 4′-CH₂—O—N(CH₃)-2′ (see published U.S. PatentApplication US2004-0171570, published Sep. 2, 2004); 4′-CH₂—N(R)—O-2′(see U.S. Pat. No. 7,427,672, issued on Sep. 23, 2008); 4′-CH₂—C(CH₃)-2′and 4′-CH₂—C(═CH₂)-2′ (see PCT/US2008/066154); and wherein R is,independently, H, C₁-C₁₂ alkyl, or a protecting group.

In certain embodiments, the present invention provides modifiednucleosides comprising modified sugar moieties that are not bicyclicsugar moieties. Certain such modified nucleosides are known. In certainembodiments, the sugar ring of a nucleoside may be modified at anyposition. Examples of sugar modifications useful in this inventioninclude, but are not limited to compounds comprising a sugar substituentgroup selected from: OH, F, O-alkyl, S-alkyl, N-alkyl, orO-alkyl-O-alkyl, wherein the alkyl, alkenyl and alkynyl may besubstituted or unsubstituted C₁ to C₁₀ alkyl or C₂ to C₁₀ alkenyl andalkynyl. In certain such embodiments, such substituents are at the 2′position of the sugar.

In certain embodiments, modified nucleosides comprise a substituent atthe 2′ position of the sugar. In certain embodiments, such substituentsare selected from among: a halide (including, but not limited to F),allyl, amino, azido, thio, O-allyl, O—C₁-C₁₀ alkyl, —OCF₃,O—(CH₂)₂—O—CH₃, 2′-O(CH₂)₂SCH₃, O—(CH₂)₂—O—N(R_(m))(R_(n)), orO—CH2-C(═O)—N(R_(m))(R_(n)), where each R_(m) and R_(n) is,independently, H or substituted or unsubstituted C₁-C₁₀ alkyl.

In certain embodiments, modified nucleosides suitable for use in thepresent invention are: 2-methoxyethoxy, 2′-O-methyl (2′-O—CH₃),2′-fluoro (2′-F).

In certain embodiments, modified nucleosides having a substituent groupat the 2′-position selected from: O[(CH₂)_(n)O]_(m)CH₃, O(CH₂)_(n)NH₂,O(CH₂)_(n)CH₃, O(CH₂)_(n)ONH₂, OCH₂C(═O)N(H)CH₃, andO(CH₂)_(n)ON[(CH₂)CH₃]2, where n and m are from 1 to about 10. Other2′-sugar substituent groups include: C₁ to C₁₀ alkyl, substituted alkyl,alkenyl, alkynyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH₃,OCN, Cl, Br, CN, CF₃, OCF₃, SOCH₃, SO₂CH₃, ONO₂, NO₂, N₃, NH₂,heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino,substituted silyl, an RNA cleaving group, a reporter group, anintercalator, a group for improving pharmacokinetic properties, or agroup for improving the pharmacodynamic properties of an oligomericcompound, and other substituents having similar properties.

In certain embodiments, modified nucleosides comprise a 2′-MOE sidechain (Baker et al., J. Biol. Chem., 1997, 272, 11944-12000). Such2′-MOE substitution have been described as having improved bindingaffinity compared to unmodified nucleosides and to other modifiednucleosides, such as 2′-O-methyl, O-propyl, and O-aminopropyl.Oligonucleotides having the 2′-MOE substituent also have been shown tobe antisense inhibitors of gene expression with promising features forin vivo use (Martin, P., Helv. Chim. Acta, 1995, 78, 486-504; Altmann etal., Chimia, 1996, 50, 168-176; Altmann et al., Biochem. Soc. Trans.,1996, 24, 630-637; and Altmann et al., Nucleosides Nucleotides, 1997,16, 917-926).

In certain embodiments, 2′-sugar substituent groups are in either thearabino (up) position or ribo (down) position. In certain suchembodiments, a 2′-arabino modification is 2′-F arabino (FANA). Similarmodifications can also be made at other positions on the sugar,particularly the 3′ position of the sugar on a 3′ terminal nucleoside orin 2′-5′ linked oligonucleotides and the 5′ position of 5′ terminalnucleotide.

In certain embodiments, nucleosides suitable for use in the presentinvention have sugar surrogates such as cyclobutyl in place of theribofuranosyl sugar. Representative U.S. patents that teach thepreparation of such modified sugar structures include, but are notlimited to, U.S.: 4,981,957; 5,118,800; 5,319,080; 5,359,044; 5,393,878;5,446,137; 5,466,786; 5,514,785; 5,519,134; 5,567,811; 5,576,427;5,591,722; 5,597,909; 5,610,300; 5,627,053; 5,639,873; 5,646,265;5,658,873; 5,670,633; 5,792,747; and 5,700,920, each of which is hereinincorporated by reference in its entirety.

In certain embodiments, the present invention provides nucleosidescomprising a modification at the 2′-position of the sugar. In certainembodiments, the invention provides nucleosides comprising amodification at the 5′-position of the sugar. In certain embodiments,the invention provides nucleosides comprising modifications at the2′-position and the 5′-position of the sugar. In certain embodiments,modified nucleosides may be useful for incorporation intooligonucleotides. In certain embodiment, modified nucleosides areincorporated into oligonucleosides at the 5′-end of the oligonucleotide.

b. Certain Internucleoside Linkages

Antisense oligonucleotides of the present invention can optionallycontain one or more modified internucleoside linkages. The two mainclasses of linking groups are defined by the presence or absence of aphosphorus atom. Representative phosphorus containing linkages include,but are not limited to, phosphodiesters (P═O), phosphotriesters,methylphosphonates, phosphoramidate, and phosphorothioates (P═S).Representative non-phosphorus containing linking groups include, but arenot limited to, methylenemethylimino (—CH2-N(CH3)-O—CH2-), thiodiester(—O—C(O)—S—), thionocarbamate (—O—C(O)(NH)—S—); siloxane (—O—Si(H)2-O—);and N,N′-dimethylhydrazine (—CH2-N(CH3)-N(CH3)-). Oligonucleotideshaving non-phosphorus linking groups are referred to asoligonucleosides. Modified linkages, compared to natural phosphodiesterlinkages, can be used to alter, typically increase, nuclease resistanceof the oligonucleotides. In certain embodiments, linkages having achiral atom can be prepared as racemic mixtures, as separateenantiomers. Representative chiral linkages include, but are not limitedto, alkylphosphonates and phosphorothioates. Methods of preparation ofphosphorous-containing and non-phosphorous-containing linkages are wellknown to those skilled in the art.

The antisense oligonucleotides described herein contain one or moreasymmetric centers and thus give rise to enantiomers, diastereomers, andother stereoisomeric configurations that may be defined, in terms ofabsolute stereochemistry, as (R) or (S), such as for sugar anomers, oras (D) or (L) such as for amino acids et al. Included in the antisensecompounds provided herein are all such possible isomers, as well astheir racemic and optically pure forms.

In certain embodiments, antisense oligonucleotides have at least onemodified internucleoside linkage. In certain embodiments, antisenseoligonucleotides have at least 2 modified internucleoside linkages. Incertain embodiments, antisense oligonucleotides have at least 3 modifiedinternucleoside linkages. In certain embodiments, antisenseoligonucleotides have at least 10 modified internucleoside linkages. Incertain embodiments, each internucleoside linkage of an antisenseoligonucleotide is a modified internucleoside linkage. In certainembodiments, such modified internucleoside linkages are phosphorothioatelinkages.

c. Lengths

In certain embodiments, the present invention provides antisenseoligonucleotides of any of a variety of ranges of lengths. In certainembodiments, the invention provides antisense compounds or antisenseoligonucleotides comprising or consisting of X-Y linked nucleosides,where X and Y are each independently selected from 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,and 50; provided that X<Y. For example, in certain embodiments, theinvention provides antisense compounds or antisense oligonucleotidescomprising or consisting of: 8-9, 8-10, 8-11, 8-12, 8-13, 8-14, 8-15,8-16, 8-17, 8-18, 8-19, 8-20, 8-21, 8-22, 8-23, 8-24, 8-25, 8-26, 8-27,8-28, 8-29, 8-30, 9-10, 9-11, 9-12, 9-13, 9-14, 9-15, 9-16, 9-17, 9-18,9-19, 9-20, 9-21, 9-22, 9-23, 9-24, 9-25, 9-26, 9-27, 9-28, 9-29, 9-30,10-11, 10-12, 10-13, 10-14, 10-15, 10-16, 10-17, 10-18, 10-19, 10-20,10-21, 10-22, 10-23, 10-24, 10-25, 10-26, 10-27, 10-28, 10-29, 10-30,11-12, 11-13, 11-14, 11-15, 11-16, 11-17, 11-18, 11-19, 11-20, 11-21,11-22, 11-23, 11-24, 11-25, 11-26, 11-27, 11-28, 11-29, 11-30, 12-13,12-14, 12-15, 12-16, 12-17, 12-18, 12-19, 12-20, 12-21, 12-22, 12-23,12-24, 12-25, 12-26, 12-27, 12-28, 12-29, 12-30, 13-14, 13-15, 13-16,13-17, 13-18, 13-19, 13-20, 13-21, 13-22, 13-23, 13-24, 13-25, 13-26,13-27, 13-28, 13-29, 13-30, 14-15, 14-16, 14-17, 14-18, 14-19, 14-20,14-21, 14-22, 14-23, 14-24, 14-25, 14-26, 14-27, 14-28, 14-29, 14-30,15-16, 15-17, 15-18, 15-19, 15-20, 15-21, 15-22, 15-23, 15-24, 15-25,15-26, 15-27, 15-28, 15-29, 15-30, 16-17, 16-18, 16-19, 16-20, 16-21,16-22, 16-23, 16-24, 16-25, 16-26, 16-27, 16-28, 16-29, 16-30, 17-18,17-19, 17-20, 17-21, 17-22, 17-23, 17-24, 17-25, 17-26, 17-27, 17-28,17-29, 17-30, 18-19, 18-20, 18-21, 18-22, 18-23, 18-24, 18-25, 18-26,18-27, 18-28, 18-29, 18-30, 19-20, 19-21, 19-22, 19-23, 19-24, 19-25,19-26, 19-29, 19-28, 19-29, 19-30, 20-21, 20-22, 20-23, 20-24, 20-25,20-26, 20-27, 20-28, 20-29, 20-30, 21-22, 21-23, 21-24, 21-25, 21-26,21-27, 21-28, 21-29, 21-30, 22-23, 22-24, 22-25, 22-26, 22-27, 22-28,22-29, 22-30, 23-24, 23-25, 23-26, 23-27, 23-28, 23-29, 23-30, 24-25,24-26, 24-27, 24-28, 24-29, 24-30, 25-26, 25-27, 25-28, 25-29, 25-30,26-27, 26-28, 26-29, 26-30, 27-28, 27-29, 27-30, 28-29, 28-30, or 29-30linked nucleosides.

In certain embodiments, antisense compounds or antisenseoligonucleotides of the present invention are 15 nucleosides in length.In certain embodiments, antisense compounds or antisenseoligonucleotides of the present invention are 16 nucleosides in length.In certain embodiments, antisense compounds or antisenseoligonucleotides of the present invention are 17 nucleosides in length.In certain embodiments, antisense compounds or antisenseoligonucleotides of the present invention are 18 nucleosides in length.In certain embodiments, antisense compounds or antisenseoligonucleotides of the present invention are 19 nucleosides in length.In certain embodiments, antisense compounds or antisenseoligonucleotides of the present invention are 20 nucleosides in length.

d. Certain Oligonucleotide Motifs

In certain embodiments, antisense oligonucleotides have chemicallymodified subunits arranged in specific orientations along their length.In certain embodiments, antisense oligonucleotides of the invention arefully modified. In certain embodiments, antisense oligonucleotides ofthe invention are uniformly modified. In certain embodiments, antisenseoligonucleotides of the invention are uniformly modified and eachnucleoside comprises a 2′-MOE sugar moiety. In certain embodiments,antisense oligonucleotides of the invention are uniformly modified andeach nucleoside comprises a 2′-OMe sugar moiety. In certain embodiments,antisense oligonucleotides of the invention are uniformly modified andeach nucleoside comprises a morpholino sugar moiety.

In certain embodiments, oligonucleotides of the invention comprise analternating motif. In certain such embodiments, the alternatingmodification types are selected from among 2′-MOE, 2′-F, a bicyclicsugar-modified nucleoside, and DNA (unmodified 2′-deoxy). In certainsuch embodiments, each alternating region comprises a single nucleoside.

In certain embodiments, oligonucleotides of the invention comprise oneor more block of nucleosides of a first type and one or more block ofnucleosides of a second type.

In certain embodiments, one or more alternating regions in analternating motif include more than a single nucleoside of a type. Forexample, oligomeric compounds of the present invention may include oneor more regions of any of the following nucleoside motifs:

Nu₁ Nu₁ Nu₂ Nu₂ Nu₁ Nu₁;

Nu₁ Nu₂ Nu₂ Nu₁ Nu₂ Nu₂;

Nu₁ Nu₁ Nu₂ Nu₁ Nu₁ Nu₂;

Nu₁ Nu₂ Nu₂ Nu₁ Nu₂ Nu₁ Nu₁ Nu₂ Nu₂;

Nu₁ Nu₂ Nu₁ Nu₂ Nu₁ Nu₁;

Nu₁ Nu₁ Nu₂ Nu₁ Nu₂ Nu₁ Nu₂;

Nu₁ Nu₂ Nu₁ Nu₂ Nu₁ Nu₁;

Nu₁ Nu₂ Nu₂ Nu₁ Nu₁ Nu₂ Nu₂ Nu₁ Nu₂ Nu₁ Nu₂ Nu₁ Nu₁;

Nu₂ Nu₁ Nu₂ Nu₂ Nu₁ Nu₁ Nu₂ Nu₂ Nu₁ Nu₂ Nu₁Nu₂ Nu₁ Nu₁; or

Nu₁ Nu₂Nu₁ Nu₂ Nu₂ Nu₁ Nu₁ Nu₂ Nu₂ Nu₁ Nu₂ Nu₁ Nu₂ Nu₁ Nu₁;

wherein Nu₁ is a nucleoside of a first type and Nu₂ is a nucleoside of asecond type. In certain embodiments, one of Nu₁ and Nu₂ is a 2′-MOEnucleoside and the other of Nu₁ and Nu₂ is a selected from: a 2′-OMemodified nucleoside, BNA, and an unmodified DNA or RNA nucleoside.

2. Oligomeric Compounds

In certain embodiments, the present invention provides oligomericcompounds. In certain embodiments, oligomeric compounds are comprisedonly of an oligonucleotide. In certain embodiments, an oligomericcompound comprises an oligonucleotide and one or more conjugate and/orterminal group. Such conjugate and/or terminal groups may be added tooligonucleotides having any of the chemical motifs discussed above.Thus, for example, an oligomeric compound comprising an oligonucleotidehaving region of alternating nucleosides may comprise a terminal group.

a. Certain Conjugate Groups

In certain embodiments, oligonucleotides of the present invention aremodified by attachment of one or more conjugate groups. In general,conjugate groups modify one or more properties of the attachedoligomeric compound including but not limited to, pharmacodynamics,pharmacokinetics, stability, binding, absorption, cellular distribution,cellular uptake, charge and clearance. Conjugate groups are routinelyused in the chemical arts and are linked directly or via an optionalconjugate linking moiety or conjugate linking group to a parent compoundsuch as an oligomeric compound, such as an oligonucleotide. Conjugategroups includes without limitation, intercalators, reporter molecules,polyamines, polyamides, polyethylene glycols, thioethers, polyethers,cholesterols, thiocholesterols, cholic acid moieties, folate, lipids,phospholipids, biotin, phenazine, phenanthridine, anthraquinone,adamantane, acridine, fluoresceins, rhodamines, coumarins and dyes.Certain conjugate groups have been described previously, for example:cholesterol moiety (Letsinger et al., Proc. Natl. Acad. Sci. USA, 1989,86, 6553-6556), cholic acid (Manoharan et al., Bioorg. Med. Chem. Let.,1994, 4, 1053-1060), a thioether, e.g., hexyl-S-tritylthiol (Manoharanet al., Ann. N.Y. Acad. Sci., 1992, 660, 306-309; Manoharan et al.,Bioorg. Med. Chem. Let., 1993, 3, 2765-2770), a thiocholesterol(Oberhauser et al., Nucl. Acids Res., 1992, 20, 533-538), an aliphaticchain, e.g., do-decan-diol or undecyl residues (Saison-Behmoaras et al.,EMBO J., 1991, 10, 1111-1118; Kabanov et al., FEBS Lett., 1990, 259,327-330; Svinarchuk et al., Biochimie, 1993, 75, 49-54), a phospholipid,e.g., di-hexadecyl-rac-glycerol or triethyl-ammonium1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate (Manoharan et al.,Tetrahedron Lett., 1995, 36, 3651-3654; Shea et al., Nucl. Acids Res.,1990, 18, 3777-3783), a polyamine or a polyethylene glycol chain(Manoharan et al., Nucleosides & Nucleotides, 1995, 14, 969-973), oradamantane acetic acid (Manoharan et al., Tetrahedron Lett., 1995, 36,3651-3654), a palmityl moiety (Mishra et al., Biochim. Biophys. Acta,1995, 1264, 229-237), or an octadecylamine orhexylamino-carbonyl-oxycholesterol moiety (Crooke et al., J. Pharmacol.Exp. Ther., 1996, 277, 923-937).

In certain embodiments, a conjugate group comprises an active drugsubstance, for example, aspirin, warfarin, phenylbutazone, ibuprofen,suprofen, fen-bufen, ketoprofen, (S)-(+)-pranoprofen, carprofen,dansylsarcosine, 2,3,5-triiodobenzoic acid, flufenamic acid, folinicacid, a benzothiadiazide, chlorothiazide, a diazepine, indo-methicin, abarbiturate, a cephalosporin, a sulfa drug, an antidiabetic, anantibacterial or an antibiotic. Oligonucleotide-drug conjugates andtheir preparation are described in U.S. patent application Ser. No.09/334,130.

Representative U.S. patents that teach the preparation ofoligonucleotide conjugates include, but are not limited to, U.S.:4,828,979; 4,948,882; 5,218,105; 5,525,465; 5,541,313; 5,545,730;5,552,538; 5,578,717, 5,580,731; 5,580,731; 5,591,584; 5,109,124;5,118,802; 5,138,045; 5,414,077; 5,486,603; 5,512,439; 5,578,718;5,608,046; 4,587,044; 4,605,735; 4,667,025; 4,762,779; 4,789,737;4,824,941; 4,835,263; 4,876,335; 4,904,582; 4,958,013; 5,082,830;5,112,963; 5,214,136; 5,082,830; 5,112,963; 5,214,136; 5,245,022;5,254,469; 5,258,506; 5,262,536; 5,272,250; 5,292,873; 5,317,098;5,371,241, 5,391,723; 5,416,203, 5,451,463; 5,510,475; 5,512,667;5,514,785; 5,565,552; 5,567,810; 5,574,142; 5,585,481; 5,587,371;5,595,726; 5,597,696; 5,599,923; 5,599,928 and 5,688,941.

Conjugate groups may be attached to either or both ends of anoligonucleotide (terminal conjugate groups) and/or at any internalposition.

b. Terminal Groups

In certain embodiments, oligomeric compounds comprise terminal groups atone or both ends. In certain embodiments, a terminal group may compriseany of the conjugate groups discussed above. In certain embodiments,terminal groups may comprise additional nucleosides and/or invertedabasic nucleosides. In certain embodiments, a terminal group is astabilizing group.

In certain embodiments, oligomeric compounds comprise one or moreterminal stabilizing group that enhances properties such as for examplenuclease stability. Included in stabilizing groups are cap structures.The terms “cap structure” or “terminal cap moiety,” as used herein,refer to chemical modifications, which can be attached to one or both ofthe termini of an oligomeric compound. Certain such terminalmodifications protect the oligomeric compounds having terminal nucleicacid moieties from exonuclease degradation, and can help in deliveryand/or localization within a cell. The cap can be present at the5′-terminus (5′-cap) or at the 3′-terminus (3′-cap) or can be present onboth termini. (for more details see Wincott et al., International PCTpublication No. WO 97/26270; Beaucage and Tyer, 1993, Tetrahedron 49,1925; U.S. Patent Application Publication No. US 2005/0020525; and WO03/004602.

In certain embodiments, one or more additional nucleosides is added toone or both terminal ends of an oligonucleotide of an oligomericcompound. Such additional terminal nucleosides are referred to herein asterminal-group nucleosides. In a double-stranded compound, suchterminal-group nucleosides are terminal (3′ and/or 5′) overhangs. In thesetting of double-stranded antisense compounds, such terminal-groupnucleosides may or may not be complementary to a target nucleic acid. Incertain embodiments, the terminal group is a non-nucleoside terminalgroup. Such non-terminal groups may be any terminal group other than anucleoside.

3. Antisense

In certain embodiments, oligomeric compounds of the present inventionare antisense compounds. Accordingly, in such embodiments, oligomericcompounds hybridize with a target nucleic acid, resulting in anantisense activity.

a. Hybridization

In certain embodiments, the invention provides antisense compounds thatspecifically hybridize to a target nucleic acid when there is asufficient degree of complementarity to avoid non-specific binding ofthe antisense compound to non-target nucleic acid sequences underconditions in which specific binding is desired, i.e., underphysiological conditions in the case of in vivo assays or therapeutictreatment, and under conditions in which assays are performed in thecase of in vitro assays.

Thus, “stringent hybridization conditions” or “stringent conditions”means conditions under which an antisense compounds hybridize to atarget sequence, but to a minimal number of other sequences. Stringentconditions are sequence-dependent and will be different in differentcircumstances, and “stringent conditions” under which antisenseoligonucleotides hybridize to a target sequence are determined by thenature and composition of the antisense oligonucleotides and the assaysin which they are being investigated.

It is understood in the art that incorporation of nucleotide affinitymodifications may allow for a greater number of mismatches compared toan unmodified compound. Similarly, certain nucleobase sequences may bemore tolerant to mismatches than other nucleobase sequences. One ofordinary skill in the art is capable of determining an appropriatenumber of mismatches between oligonucleotides, or between an antisenseoligonucleotide and a target nucleic acid, such as by determiningmelting temperature (Tm). Tm or ΔTm can be calculated by techniques thatare familiar to one of ordinary skill in the art. For example,techniques described in Freier et al. (Nucleic Acids Research, 1997, 25,22: 4429-4443) allow one of ordinary skill in the art to evaluatenucleotide modifications for their ability to increase the meltingtemperature of an RNA:DNA duplex.

b. pre-mRNA Processing

In certain embodiments, antisense compounds provided herein arecomplementary to a pre-mRNA. In certain embodiments, such antisensecompounds alter splicing of the pre-mRNA. In certain such embodiments,the ratio of one variant of a mature mRNA corresponding to a targetpre-mRNA to another variant of that mature mRNA is altered. In certainsuch embodiments, the ratio of one variant of a protein expressed fromthe target pre-mRNA to another variant of the protein is altered.Certain oligomeric compounds and nucleobase sequences that may be usedto alter splicing of a pre-mRNA may be found for example in U.S. Pat.No. 6,210,892; U.S. Pat. No. 5,627,274; U.S. Pat. Nos. 5,665,593;5,916,808; U.S. Pat. No. 5,976,879; US2006/0172962; US2007/002390;US2005/0074801; US2007/0105807; US2005/0054836; WO 2007/090073;WO2007/047913, Hua et al., PLoS Biol 5(4):e73; Vickers et al., J.Immunol. 2006 Mar. 15; 176(6):3652-61; and Hua et al., American J. ofHuman Genetics (April 2008) 82, 1-15, each of which is herebyincorporated by reference in its entirety for any purpose. In certainembodiments antisense sequences that alter splicing are modifiedaccording to motifs of the present invention.

Antisense is an effective means for modulating the expression of one ormore specific gene products and is uniquely useful in a number oftherapeutic, diagnostic, and research applications. Provided herein areantisense compounds useful for modulating gene expression via antisensemechanisms of action, including antisense mechanisms based on targetoccupancy. In one aspect, the antisense compounds provided hereinmodulate splicing of a target gene. Such modulation includes promotingor inhibiting exon inclusion. Further provided herein are antisensecompounds targeted to cis splicing regulatory elements present inpre-mRNA molecules, including exonic splicing enhancers, exonic splicingsilencers, intronic splicing enhancers and intronic splicing silencers.Disruption of cis splicing regulatory elements is thought to altersplice site selection, which may lead to an alteration in thecomposition of splice products.

Processing of eukaryotic pre-mRNAs is a complex process that requires amultitude of signals and protein factors to achieve appropriate mRNAsplicing. Exon definition by the spliceosome requires more than thecanonical splicing signals which define intron-exon boundaries. One suchadditional signal is provided by cis-acting regulatory enhancer andsilencer sequences. Exonic splicing enhancers (ESE), exonic splicingsilencers (ESS), intronic splicing enhancers (ISE) and intron splicingsilencers (ISS) have been identified which either repress or enhanceusage of splice donor sites or splice acceptor sites, depending on theirsite and mode of action (Yeo et al. 2004, Proc. Natl. Acad. Sci. U.S.A.101(44):15700-15705). Binding of specific proteins (trans factors) tothese regulatory sequences directs the splicing process, eitherpromoting or inhibiting usage of particular splice sites and thusmodulating the ratio of splicing products (Scamborova et al. 2004, Mol.Cell. Biol. 24(5):1855-1869; Hovhannisyan and Carstens, 2005, Mol. Cell.Biol. 25(1):250-263; Minovitsky et al. 2005, Nucleic Acids Res.33(2):714-724).

4. Pharmaceutical Compositions

In certain embodiments, the present invention provides pharmaceuticalcompositions comprising one or more antisense compound. In certainembodiments, such pharmaceutical composition comprises a sterile salinesolution and one or more antisense compound. In certain embodiments,such pharmaceutical composition consists of a sterile saline solutionand one or more antisense compound.

In certain embodiments, antisense compounds may be admixed withpharmaceutically acceptable active and/or inert substances for thepreparation of pharmaceutical compositions or formulations. Compositionsand methods for the formulation of pharmaceutical compositions depend ona number of criteria, including, but not limited to, route ofadministration, extent of disease, or dose to be administered.

In certain embodiments antisense compounds, can be utilized inpharmaceutical compositions by combining such oligomeric compounds witha suitable pharmaceutically acceptable diluent or carrier. Apharmaceutically acceptable diluent includes phosphate-buffered saline(PBS). PBS is a diluent suitable for use in compositions to be deliveredparenterally. Accordingly, in certain embodiments, employed in themethods described herein is a pharmaceutical composition comprising anantisense compound and a pharmaceutically acceptable diluent. In certainembodiments, the pharmaceutically acceptable diluent is PBS. In certainembodiments, the pharmaceutically acceptable diluent is artificial CSF.

Pharmaceutical compositions comprising antisense compounds encompass anypharmaceutically acceptable salts, esters, or salts of such esters. Incertain embodiments, pharmaceutical compositions comprising antisensecompounds comprise one or more oligonucleotide which, uponadministration to an animal, including a human, is capable of providing(directly or indirectly) the biologically active metabolite or residuethereof. Accordingly, for example, the disclosure is also drawn topharmaceutically acceptable salts of antisense compounds, prodrugs,pharmaceutically acceptable salts of such prodrugs, and otherbioequivalents. Suitable pharmaceutically acceptable salts include, butare not limited to, sodium and potassium salts.

A prodrug can include the incorporation of additional nucleosides at oneor both ends of an oligomeric compound which are cleaved by endogenousnucleases within the body, to form the active antisense oligomericcompound.

Lipid-based vectors have been used in nucleic acid therapies in avariety of methods. For example, in one method, the nucleic acid isintroduced into preformed liposomes or lipoplexes made of mixtures ofcationic lipids and neutral lipids. In another method, DNA complexeswith mono- or poly-cationic lipids are formed without the presence of aneutral lipid.

Certain preparations are described in Akinc et al., Nature Biotechnology26, 561-569 (1 May 2008), which is herein incorporated by reference inits entirety.

In certain embodiments, the pharmaceutically acceptable diluent isartificial CSF. In certain embodiments, artificial CSF is commerciallyavailable. In certain embodiments, artificial CSF is prepared accordingto a formulation provided by Harvard Apparatus, Inc. In certainembodiments, each 1 mL of artificial CSF contains the followingingredients:

Ingredients Grade Quantity/ml Sodium dihydrogen phosphate dihydrate USP,Ph. Eur. 0.050 mg Sodium phosphate dibasic anhydrous USP, Ph. Eur. 0.097mg Sodium chloride USP, Ph. Eur. 8.766 mg Potassium chloride USP, Ph.Eur. 0.224 mg Calcium chloride dihydrate USP, Ph. Eur. 0.206 mgMagnesium chloride hexahydrate USP, Ph. Eur. 0.163 mg Sodium hydroxideNF, Ph. Eur. As needed Hydrochloric acid NF, Ph. Eur. As needed Waterfor Injection USP/Ph. Eur. Q.S.

In certain embodiments, the artificial CSF formulation vehicle comprises1 mM phosphate buffer at pH 7.2, adequate sodium chloride to beisotonic, and physiological levels of electrolytes (e.g. potassium,calcium, and magnesium).

5. Certain Methods of Calculating the Amount of CSF Protein in a Subject

In certain embodiments, the present disclosure provides methodscomprising measuring the amount of SMN protein in the cerebrospinalfluid of a subject. In certain embodiments, the subject has SMA. Incertain embodiments, the method of determining the amount of SMN proteinin a biological sample, e.g. cerebrospinal fluid, comprises (a)collecting a biological sample from a subject (e.g. cerebrospinalfluid), (b) contacting the biological sample with a capture antibody,(c) contacting the biological sample with a detection antibody, and (d)measuring the amount of detection antibody in the biological sample andcalculating the amount of SMN protein in the biological sample.

In certain embodiments, the present disclosure provides a method ofdetermining the amount of SMN protein in a biological sample comprising:(a) collecting a biological sample from a subject; (b) contacting thebiological sample with a capture antibody; (c) contacting the biologicalsample with a detection antibody; (d) measuring the amount of detectionantibody in the biological sample; and (e) calculating the amount of SMNprotein in the biological sample.

6. Administration to a Subject

In certain embodiments, pharmaceutical compositions comprising one ormore antisense compound are administered to a subject. In certainembodiments, such pharmaceutical compositions are administered byinjection. In certain embodiments, such pharmaceutical compositions areadministered by infusion.

In certain embodiments, pharmaceutical compositions are administered byinjection or infusion into the CSF. In certain such embodiments,pharmaceutical compositions are administered by direct injection orinfusion into the spine. In certain embodiments, pharmaceuticalcompositions are administered by injection or infusion into the brain.In certain embodiments, pharmaceutical compositions are administered byintrathecal injection or infusion rather than into the spinal cordtissue itself. Without being limited as to theory, in certainembodiments, the antisense compound released into the surrounding CSFand may penetrate into the spinal cord parenchyma. An additionaladvantage of intrathecal delivery is that the intrathecal route mimicslumbar puncture administration (i.e., spinal tap) already in routine usein humans.

In certain embodiments, pharmaceutical compositions are administered byintracerebroventricular (ICV) injection or infusion.Intracerebroventricular, or intraventricular, delivery of apharmaceutical composition comprising one or more antisense compoundsmay be performed in any one or more of the brain's ventricles, which arefilled with cerebrospinal fluid (CSF). CSF is a clear fluid that fillsthe ventricles, is present in the subarachnoid space, and surrounds thebrain and spinal cord. CSF is produced by the choroid plexuses and viathe weeping or transmission of tissue fluid by the brain into theventricles. The choroid plexus is a structure lining the floor of thelateral ventricle and the roof of the third and fourth ventricles.Certain studies have indicated that these structures are capable ofproducing 400-600 ccs of fluid per day consistent with an amount to fillthe central nervous system spaces four times in a day. In adult humans,the volume of this fluid has been calculated to be from 125 to 150 ml(4-5 oz). The CSF is in continuous formation, circulation andabsorption. Certain studies have indicated that approximately 430 to 450ml (nearly 2 cups) of CSF may be produced every day. Certaincalculations estimate that production equals approximately 0.35 ml perminute in adults and 0.15 per minute in infant humans. The choroidplexuses of the lateral ventricles produce the majority of CSF. It flowsthrough the foramina of Monro into the third ventricle where it is addedto by production from the third ventricle and continues down through theaqueduct of Sylvius to the fourth ventricle. The fourth ventricle addsmore CSF; the fluid then travels into the subarachnoid space through theforamina of Magendie and Luschka. It then circulates throughout the baseof the brain, down around the spinal cord and upward over the cerebralhemispheres. The CSF empties into the blood via the arachnoid villi andintracranial vascular sinuses.

In certain embodiments, such pharmaceutical compositions areadministered systemically. In certain embodiments, pharmaceuticalcompositions are administered subcutaneously. In certain embodiments,pharmaceutical compositions are administered intravenously. In certainembodiments, pharmaceutical compositions are administered byintramuscular injection.

In certain embodiments, pharmaceutical compositions are administeredboth directly to the CSF (e.g., IT and/or ICV injection and/or infusion)and systemically.

In certain embodiments, an antisense compound administered systemicallyenters neurons. In certain embodiments, systemically administeredantisense compounds may penetrate the blood-brain barrier, particularlyin young subjects where the blood-brain barrier is not fully formed(e.g., in subjects in eutero and/or in newborn subjects). In certainembodiments, some amount of systemically administered antisense compoundmay be taken up by nerve cells, even in subjects in which theblood-brain barrier is fully formed. For example, antisense compoundsmay enter a neuron at or near the neuromuscular junction (retrogradeuptake). In certain embodiments, such retrograde uptake results inantisense activity inside the neuron, including, but not limited to, amotor neuron, and provides a therapeutic benefit by antisense activityinside the neuron.

In certain embodiments, systemic administration provides therapeuticbenefit by antisense activity occurring in cells and/or tissues otherthan neurons. While evidence suggests that functional SMN inside neuronsis required for normal neuron function, the consequence of reducedfunctional SMN in other cells and tissues is not well characterized. Incertain embodiments, antisense activity in non-neuronal cells results inrestoration of SMN function in those non-neuronal cells, which in turnresults in therapeutic benefit.

In certain embodiments, improved SMN function in non-neuronal cellsprovides improved neuronal cell function, whether or not SMN functioninside neurons is improved. For example, in certain embodiments,systemic administration of pharmaceutical compositions of the presentinvention results in antisense activity in muscle cells. Such antisenseactivity in muscle cells may provide a benefit to the motor-neuronsassociated with that muscle cell or to neurons generally. In suchembodiments, the muscle cell having restored SMN function may provide afactor that improves neuronal viability and/or function. In certainembodiments, such antisense activity is independent of benefit fromantisense activity occurring from antisense compounds inside neurons. Incertain embodiments, systemic administration of pharmaceuticalcompositions of the present invention results in antisense activity inother non-neuronal cells, including cells not in immediate associationwith neurons. Such antisense activity in non-neuronal cells may improvefunction of neurons. For example, antisense activity in a non-neuronalcell (e.g., liver cell) may result in that cell producing a factor thatimproves function of neurons. Note: since the term “antisense activity”includes direct and indirect activities, a benefit to neuronal functionis an “antisense activity” even if no antisense compound enters theneuron.

In certain embodiments, systemic administration of a pharmaceuticalcomposition results in therapeutic benefit independent of direct orindirect antisense activities in neurons. Typically, in the setting ofSMA, neuronal function is diminished, resulting in significant symptoms.Additional symptoms may result from diminished SMN activity in othercells. Certain such symptoms may be masked by the relative severity ofsymptoms from diminished neuronal function. In certain embodiments,systemic administration results in restored or improved SMN function innon-neuronal cells. In certain such embodiments, such restored orimproved SMN function in non-neuronal cells has therapeutic benefit. Forexample, in certain instances, subjects having SMA have reduced growth.Such reduced growth may not result from diminished function in neuronalcells. Indeed, reduced growth may be related to impaired function ofcells in another organ, such as the pituitary gland, and/or may be theresult of SMN deficiencies throughout the cells of the body. In suchembodiments, systemic administration may result in improved SMN activityin pituitary cells and/or other cells, resulting in improved growth. Incertain instances, administration to the CSF restores sufficientneuronal function to allow a subject to live longer, however one or moresymptoms previously unknown because subjects typically died before suchsymptoms appeared emerges, because the subject lives longer. Certainsuch emergent symptoms may be lethal. In certain embodiments, emergentsymptoms are treated by systemic administration. Regardless ofmechanism, in certain embodiments, a variety of symptoms of SMA,including, but not limited to symptoms previously masked by more severesymptoms associated with impaired neuronal function, may be treated bysystemic administration.

In certain embodiments, systemic administration of pharmaceuticalcompositions of the present invention result in increased SMN activityin muscle cells. In certain embodiments, such improved SMN activity inmuscle cells provides therapeutic benefit. Improved SMN activity inmuscle alone has been reported to be insufficient to provide therapeuticbenefit (e.g., Gravrilina, et al., Hum Mol Genet 2008 17(8):1063-1075).In certain embodiments, the present invention provides methods thatresult improve SMN function in muscle and do provide therapeuticbenefit.

In certain instances, therapeutic benefit may be attributable toimproved SMN function in other cells (alone or in combination withmuscle cells). In certain embodiments, improved SMN function in musclealone may provide benefit.

In certain embodiments, systemic administration results in improvedsurvival.

7. Spinal Muscular Atrophy (SMA)

SMA is a genetic disorder characterized by degeneration of spinal motorneurons. SMA is caused by the homozygous loss of both functional copiesof the SMN1 gene. However, the SMN2 gene has the potential to code forthe same protein as SMN1 and thus overcome the genetic defect of SMApatients. SMN2 contains a translationally silent mutation (C→T) atposition +6 of exon 7, which results in inefficient inclusion of exon 7in SMN2 transcripts. Therefore, the predominant form of SMN2, one whichlacks exon 7, is unstable and inactive. Thus, therapeutic compoundscapable of modulating SMN2 splicing such that the percentage of SMN2transcripts containing exon 7 is increased, would be useful for thetreatment of SMA.

In certain embodiments, the present invention provides antisensecompounds complementary to a pre-mRNA encoding SMN2. In certain suchembodiments, the antisense compound alters splicing of SMN2. Certainsequences and regions useful for altering splicing of SMN2 may be foundin PCT/US06/024469, which is hereby incorporated by reference in itsentirety for any purpose. In certain embodiments, oligomeric compoundshaving any motif described herein have a nucleobase sequencecomplementary to intron 7 of SMN2. Certain such nucleobase sequences areexemplified in the non-limiting table below. In the nucleobase sequencesexemplified in the non-limiting table below, all “C” residues represent5-methylcytosines.

Sequence Length SEQ ID NO TGCTGGCAGACTTAC 15  3 CATAATGCTGGCAGA 15  4TCATAATGCTGGCAG 15  5 TTCATAATGCTGGCA 15  6 TTTCATAATGCTGGC 15  2ATTCACTTTCATAATGCTGG 20  7 TCACTTTCATAATGCTGG 18  1 CTTTCATAATGCTGG 15 8 TCATAATGCTGG 12  9 ACTTTCATAATGCTG 15 10 TTCATAATGCTG 12 11CACTTTCATAATGCT 15 12 TTTCATAATGCT 12 13 TCACTTTCATAATGC 15 14CTTTCATAATGC 12 15 TTCACTTTCATAATG 15 16 ACTTTCATAATG 12 17ATTCACTTTCATAAT 15 18 CACTTTCATAAT 12 19 GATTCACTTTCATAA 15 20TCACTTTCATAA 12 21 TTCACTTTCATA 12 22 ATTCACTTTCAT 12 23 AGTAAGATTCACTTT15 24

Antisense compounds of the present invention can be used to modulate theexpression of SMN2 in a subject, such as a human. In certainembodiments, the subject has spinal muscular atrophy. In certain suchsubjects, the SMN1 gene is absent or otherwise fails to producesufficient amounts of functional SMN protein. In certain embodiments,the antisense compounds of the present invention effectively modulatesplicing of SMN2, resulting in an increase in exon 7 inclusion in SMN2mRNA and ultimately in SMN2 protein that includes the amino acidscorresponding to exon 7. Such alternate SMN2 protein resembles wild-typeSMN protein. Antisense compounds of the present invention thateffectively modulate expression of SMN2 mRNA or protein products ofexpression are considered active antisense compounds.

Modulation of expression of SMN2 can be measured in a bodily fluid,which may or may not contain cells; tissue; or organ of the animal.Methods of obtaining samples for analysis, such as body fluids (e.g.,sputum, serum, CSF), tissues (e.g., biopsy), or organs, and methods ofpreparation of the samples to allow for analysis are well known to thoseskilled in the art. Methods for analysis of RNA and protein levels arediscussed above and are well known to those skilled in the art. Theeffects of treatment can be assessed by measuring biomarkers associatedwith the target gene expression in the aforementioned fluids, tissues ororgans, collected from an animal contacted with one or more compounds ofthe invention, by routine clinical methods known in the art.

Methods whereby bodily fluids, organs or tissues are contacted with aneffective amount of one or more of the antisense compounds orcompositions of the invention are also contemplated. Bodily fluids,organs or tissues can be contacted with one or more of the compounds ofthe invention resulting in modulation of SMN2 expression in the cells ofbodily fluids, organs or tissues. An effective amount can be determinedby monitoring the modulatory effect of the antisense compound orcompounds or compositions on target nucleic acids or their products bymethods routine to the skilled artisan.

The invention also provides an antisense compound as described herein,for use in any of the methods as described herein. For example, theinvention provides an antisense compound comprising an antisenseoligonucleotide complementary to a nucleic acid encoding human SMN2, foruse in treating a disease or condition associated with survival motorneuron protein (SMN), such as spinal muscular atrophy (SMA). As afurther example, the invention provides an antisense compound comprisingan antisense oligonucleotide complementary to a nucleic acid encodinghuman SMN2, for use in treating a disease or condition associated withsurvival motor neuron protein (SMN) by administering the antisensecompound directly into the central nervous system (CNS) or CSF.

The invention also provides the use of an antisense compound asdescribed herein in the manufacture of a medicament for use in any ofthe methods as described herein. For example, the invention provides theuse of an antisense compound comprising an antisense oligonucleotidecomplementary to a nucleic acid encoding human SMN2 in the manufactureof a medicament for treating a disease or condition associated withsurvival motor neuron protein (SMN), such as spinal muscular atrophy(SMA). As a further example, the invention provides the use of anantisense compound comprising an antisense oligonucleotide complementaryto a nucleic acid encoding human SMN2 in the manufacture of a medicamentfor treating a disease or condition associated with survival motorneuron protein (SMN) by administration of the medicament directly intothe central nervous system (CNS) or CSF.

In certain embodiments, oligomeric compounds having any motif describedherein have a nucleobase sequence complementary to exon 7 of SMN2.

In certain embodiments, oligomeric compounds having any motif describedherein have a nucleobase sequence complementary to intron 6 of SMN2.

In certain embodiments, an antisense compound comprises an antisenseoligonucleotide having a nucleobase sequence comprising at least 10nucleobases of the sequence: TCACTTTCATAATGCTGG (SEQ ID NO: 1). Incertain embodiments, an antisense oligonucleotide has a nucleobasesequence comprising at least 11 nucleobases of such sequence. In certainembodiments, an antisense oligonucleotide has a nucleobase sequencecomprising at least 12 nucleobases of such sequence. In certainembodiments, an antisense oligonucleotide has a nucleobase sequencecomprising at least 13 nucleobases of such sequence. In certainembodiments, an antisense oligonucleotide has a nucleobase sequencecomprising at least 14 nucleobases of such sequence. In certainembodiments, an antisense oligonucleotide has a nucleobase sequencecomprising at least 15 nucleobases of such sequence. In certainembodiments, an antisense oligonucleotide has a nucleobase sequencecomprising at least 16 nucleobases of such sequence. In certainembodiments, an antisense oligonucleotide has a nucleobase sequencecomprising at least 17 nucleobases of such sequence. In certainembodiments, an antisense oligonucleotide has a nucleobase sequencecomprising the nucleobases of such sequence. In certain embodiments, anantisense oligonucleotide has a nucleobase sequence consisting of thenucleobases of such sequence. In certain embodiments, an antisenseoligonucleotide consists of 10-18 linked nucleosides and has anucleobase sequence 100% identical to an equal-length portion of thesequence:

(SEQ ID NO: 1) TCACTTTCATAATGCTGG.

8. Certain Subjects

In certain embodiments, a subject has one or more indicator of SMA. Incertain embodiments, the subject has reduced electrical activity of oneor more muscles. In certain embodiments, the subject has a mutant SMN1gene. In certain embodiment, the subject's SMN1 gene is absent orincapable of producing functional SMN protein. In certain embodiments,the subject is diagnosed by a genetic test. In certain embodiments, thesubject is identified by muscle biopsy. In certain embodiments, asubject is unable to sit upright. In certain embodiments, a subject isunable to stand or walk. In certain embodiments, a subject requiresassistance to breathe and/or eat. In certain embodiment, a subject isidentified by electrophysiological measurement of muscle and/or musclebiopsy.

In certain embodiments, the subject has SMA type I. In certainembodiments, the subject has SMA type II. In certain embodiments, thesubject has SMA type III. In certain embodiments, the subject has SMAtype IV. In certain embodiments, the subject is diagnosed as having SMAin utero. In certain embodiments, the subject is diagnosed as having SMAwithin one week after birth. In certain embodiments, the subject isdiagnosed as having SMA within one month of birth. In certainembodiments, the subject is diagnosed as having SMA by 3 months of age.In certain embodiments, the subject is diagnosed as having SMA by 6months of age. In certain embodiments, the subject is diagnosed ashaving SMA by 1 year of age. In certain embodiments, the subject isdiagnosed as having SMA between 1 and 2 years of age. In certainembodiments, the subject is diagnosed as having SMA between 1 and 15years of age. In certain embodiments, the subject is diagnosed as havingSMA when the subject is older than 15 years of age.

In certain embodiments, the first dose of a pharmaceutical compositionaccording to the present invention is administered in utero. In certainsuch embodiments, the first dose is administered before completedevelopment of the blood-brain-barrier. In certain embodiments, thefirst dose is administered to the subject in utero systemically. Incertain embodiments, the first dose is administered in utero afterformation of the blood-brain-barrier. In certain embodiments, the firstdose is administered to the CSF.

In certain embodiments, the first dose of a pharmaceutical compositionaccording to the present invention is administered when the subject isless than one week old. In certain embodiments, the first dose of apharmaceutical composition according to the present invention isadministered when the subject is less than one month old. In certainembodiments, the first dose of a pharmaceutical composition according tothe present invention is administered when the subject is less than 3months old. In certain embodiments, the first dose of a pharmaceuticalcomposition according to the present invention is administered when thesubject is less than 6 months old. In certain embodiments, the firstdose of a pharmaceutical composition according to the present inventionis administered when the subject is less than one year old. In certainembodiments, the first dose of a pharmaceutical composition according tothe present invention is administered when the subject is less than 2years old. In certain embodiments, the first dose of a pharmaceuticalcomposition according to the present invention is administered when thesubject is less than 15 years old. In certain embodiments, the firstdose of a pharmaceutical composition according to the present inventionis administered when the subject is older than 15 years old.

9. Certain Doses

In certain embodiments, the present invention provides dose amounts andfrequencies. In certain embodiments, pharmaceutical compositions areadministered as a bolus injection.

In certain embodiments, pharmaceutical compositions are administered asa single IT bolus lumbar puncture injection. In certain embodiments, theIT bolus lumbar puncture injection target site for needle insertion isthe L3/L4 space. In certain embodiments, the IT bolus lumbar punctureinjection target site for needle insertion is the L3/L4 space but may be1 segment above or 1-2 segments below this level, if needed. In certainembodiments, the volume of the IT bolus lumbar puncture injection is 5mL. In certain embodiments, the volume of the IT bolus lumbar punctureinjection is 1 mL. In certain embodiments, the volume of the IT boluslumbar puncture injection is 2 mL. In certain embodiments, the volume ofthe IT bolus lumbar puncture injection is 3 mL. In certain embodiments,the volume of the IT bolus lumbar puncture injection is 4 mL. In certainembodiments, the volume of the IT bolus lumbar puncture injection is 6mL. In certain embodiments, the volume of the IT bolus lumbar punctureinjection is 7 mL. In certain embodiments, the volume of the IT boluslumbar puncture injection is 8 mL. In certain embodiments, the volume ofthe IT bolus lumbar puncture injection is 9 mL. In certain embodiments,the volume of the IT bolus lumbar puncture injection is 10 mL. Incertain embodiments, the volume of the IT bolus lumbar punctureinjection is 4.3 mL. In certain embodiments, the volume of the IT boluslumbar puncture injection is 4.5 mL.

10. Administration of Certain Doses

In certain embodiments, the dose is selected to produce a desired tissueconcentration. In certain embodiments, the desired tissue is spinal cordtissue. In certain embodiments, the desired spinal cord tissueconcentration is between 1μ/g and 10μ/g. In certain embodiments, thedesired spinal cord tissue concentration is between 1μ/g and 15μ/g. Incertain embodiments, the desired spinal cord tissue concentration isbetween 1μ/g and 14μ/g. In certain embodiments, the desired spinal cordtissue concentration is between 1μ/g and 13μ/g. In certain embodiments,the desired spinal cord tissue concentration is between 1μ/g and 12μ/g.In certain embodiments, the desired spinal cord tissue concentration isbetween 1μ/g and 11μ/g. In certain embodiments, the desired spinal cordtissue concentration is between 1μ/g and 9μ/g. In certain embodiments,the desired spinal cord tissue concentration is between 1μ/g and 8μ/g.In certain embodiments, the desired spinal cord tissue concentration isbetween 1μ/g and 7μ/g. In certain embodiments, the desired spinal cordtissue concentration is between 1μ/g and 6μ/g. In certain embodiments,the desired spinal cord tissue concentration is between 1μ/g and 5μ/g.In certain embodiments, the desired spinal cord tissue concentration isbetween 1μ/g and 4μ/g. In certain embodiments, the desired spinal cordtissue concentration is between 1μ/g and 3μ/g. In certain embodiments,the desired spinal cord tissue concentration is between 1μ/g and 2μ/g.In certain embodiments, the desired spinal cord tissue concentration isbetween 1μ/g and 30μ/g. In certain embodiments, the desired spinal cordtissue concentration is between 1μ/g and 25μ/g. In certain embodiments,the desired spinal cord tissue concentration is between 1μ/g and 20μ/g.In certain embodiments, the desired spinal cord tissue concentration isbetween 1μ/g and 18μ/g.

11. Adjustment of Certain Doses

In certain embodiments, the dose is selected to produce a desired SMNprotein concentration in the CSF and subsequent doses may be selected toincrease or decrease the concentration of SMN in the CSF. For example,in certain embodiments, a sample of CSF may be taken from a patienthaving SMA and the sample analyzed to calculate the amount of SMNprotein according to methods described herein. After calculation of theamount of baseline SMN protein, the patient is given a dose of ISIS396443. In certain embodiments, the dose given to the patient is 12 mgof ISIS 396443. After receipt of the first dose of ISIS 396443, thepatient may receive a subsequent dose of ISIS 396443.

Before receipt of the subsequent dose of ISIS 396443, a second sample ofCSF may be taken from the patient and analyzed according to the methodsor kits provided herein in order to determine the amount of SMN protein.The amount of SMN protein in the CSF may then be compared from the firstand second samples from this comparison subsequent dose frequency andamount may be adjusted. For example, if the amount of SMN proteinpresent in the second sample is much greater than the amount of SMNprotein in the first sample, the dose frequency for each subsequent doseof ISIS 396443 may be decreased. For example, if the amount of SMNprotein present in the second sample is much greater than the amount ofSMN protein in the first sample, the dose amount for each subsequentdose of ISIS 396443 may be decreased. For example, if the amount of SMNprotein present in the second sample is much greater than the amount ofSMN protein in the first sample, the dose frequency and dose amount foreach subsequent dose of ISIS 396443 may be decreased. Alternatively, ifthe amount of SMN protein present in the second sample is not muchgreater than the amount of SMN protein in the first sample, the dosefrequency for each subsequent dose of ISIS 396443 may be increased. Ifthe amount of SMN protein present in the second sample is not muchgreater than the amount of SMN protein in the first sample, the doseamount for each subsequent dose of ISIS 396443 may be increased.

12. Certain Routes of Administration

In certain embodiments, a dose is administered as an intrathecalinjection by lumbar puncture. In certain embodiments, a single dose isadministered as an intrathecal injection by lumbar puncture. In certainembodiments, a single dose of ISIS 396443 is administered as anintrathecal injection by lumbar puncture. In certain embodiments, asingle 0.1 to 15 milligram dose of ISIS 396443 is administered as anintrathecal injection by lumbar puncture. In certain embodiments, asingle 1 milligram dose of ISIS 396443 is administered as an intrathecalinjection by lumbar puncture. In certain embodiments, a single 2milligram dose of ISIS 396443 is administered as an intrathecalinjection by lumbar puncture. In certain embodiments, a single 3milligram dose of ISIS 396443 is administered as an intrathecalinjection by lumbar puncture. In certain embodiments, a single 4milligram dose of ISIS 396443 is administered as an intrathecalinjection by lumbar puncture. In certain embodiments, a single 5milligram dose of ISIS 396443 is administered as an intrathecalinjection by lumbar puncture. In certain embodiments, a single 6milligram dose of ISIS 396443 is administered as an intrathecalinjection by lumbar puncture. In certain embodiments, a single 7milligram dose of ISIS 396443 is administered as an intrathecalinjection by lumbar puncture. In certain embodiments, a single 8milligram dose of ISIS 396443 is administered as an intrathecalinjection by lumbar puncture. In certain embodiments, a single 9milligram dose of ISIS 396443 is administered as an intrathecalinjection by lumbar puncture. In certain embodiments, a single 10milligram dose of ISIS 396443 is administered as an intrathecalinjection by lumbar puncture. In certain embodiments, a single 11milligram dose of ISIS 396443 is administered as an intrathecalinjection by lumbar puncture. In certain embodiments, a single 12milligram dose of ISIS 396443 is administered as an intrathecalinjection by lumbar puncture. In certain embodiments, a single 13milligram dose of ISIS 396443 is administered as an intrathecalinjection by lumbar puncture. In certain embodiments, a single 14milligram dose of ISIS 396443 is administered as an intrathecalinjection by lumbar puncture. In certain embodiments, a single 15milligram dose of ISIS 396443 is administered as an intrathecalinjection by lumbar puncture.

In certain embodiments, a single 4.8 milligram dose of ISIS 396443 isadministered as an intrathecal injection by lumbar puncture. In certainembodiments, a single 5.16 milligram dose of ISIS 396443 is administeredas an intrathecal injection by lumbar puncture. In certain embodiments,a single 5.40 milligram dose of ISIS 396443 is administered as anintrathecal injection by lumbar puncture. In certain embodiments, asingle 7.2 milligram dose of ISIS 396443 is administered as anintrathecal injection by lumbar puncture. In certain embodiments, asingle 7.74 milligram dose of ISIS 396443 is administered as anintrathecal injection by lumbar puncture. In certain embodiments, asingle 8.10 milligram dose of ISIS 396443 is administered as anintrathecal injection by lumbar puncture.

In certain embodiments, a single 9.6 milligram dose of ISIS 396443 isadministered as an intrathecal injection by lumbar puncture. In certainembodiments, a single 10.32 milligram dose of ISIS 396443 isadministered as an intrathecal injection by lumbar puncture. In certainembodiments, a single 10.80 milligram dose of ISIS 396443 isadministered as an intrathecal injection by lumbar puncture. In certainembodiments, a single 11.30 milligram dose of ISIS 396443 isadministered as an intrathecal injection by lumbar puncture. In certainembodiments, a single 12 milligram dose of ISIS 396443 is administeredas an intrathecal injection by lumbar puncture. In certain embodiments,a single 12.88 milligram dose of ISIS 396443 is administered as anintrathecal injection by lumbar puncture. In certain embodiments, asingle 13.5 milligram dose of ISIS 396443 is administered as anintrathecal injection by lumbar puncture. In certain embodiments, asingle 14.13 milligram dose of ISIS 396443 is administered as anintrathecal injection by lumbar puncture.

In certain embodiments, a single 10 milligram dose of ISIS 396443 isadministered as an intrathecal injection by lumbar puncture. In certainembodiments, a single 11 milligram dose of ISIS 396443 is administeredas an intrathecal injection by lumbar puncture. In certain embodiments,a single 12 milligram dose of ISIS 396443 is administered as anintrathecal injection by lumbar puncture. In certain embodiments, asingle 13 milligram dose of ISIS 396443 is administered as anintrathecal injection by lumbar puncture. In certain embodiments, asingle 14 milligram dose of ISIS 396443 is administered as anintrathecal injection by lumbar puncture. In certain embodiments, asingle 15 milligram dose of ISIS 396443 is administered as anintrathecal injection by lumbar puncture. In certain embodiments, asingle 16 milligram dose of ISIS 396443 is administered as anintrathecal injection by lumbar puncture. In certain embodiments, asingle 17 milligram dose of ISIS 396443 is administered as anintrathecal injection by lumbar puncture. In certain embodiments, asingle 18 milligram dose of ISIS 396443 is administered as anintrathecal injection by lumbar puncture. In certain embodiments, asingle 19 milligram dose of ISIS 396443 is administered as anintrathecal injection by lumbar puncture. In certain embodiments, asingle 20 milligram dose of ISIS 396443 is administered as anintrathecal injection by lumbar puncture.

In certain embodiments, where a dose of ISIS 396443 is administered asan intrathecal injection by lumbar puncture the use of a smaller gaugeneedle may reduce or ameliorate one or more symptoms associated with alumbar puncture procedure. In certain embodiments, symptoms associatedwith a lumbar puncture include, but are not limited to, post-lumbarpuncture syndrome, headache, back pain, pyrexia, constipation, nausea,vomiting, and puncture site pain. In certain embodiments, use of a 24 or25 gauge needle for the lumbar puncture reduces or ameliorates one ormore post lumbar puncture symptoms. In certain embodiments, use of a 21,22, 23, 24 or 25 gauge needle for the lumbar puncture reduces orameliorates post-lumbar puncture syndrome, headache, back pain, pyrexia,constipation, nausea, vomiting, and/or puncture site pain.

13. Certain Dose Concentrations and Injection Volumes

In certain embodiments, an active drug product, e.g. ISIS 396443, iscombined with one or more pharmaceutically acceptable excipients ordiluents. In certain embodiments, an active drug product, e.g. ISIS396443, is combined with an artificial CSF diluent. In certainembodiments, ISIS 396443 is combined with an artificial CSF diluent. Incertain embodiments, the concentration of ISIS 396443 in an artificialCSF diluent is 0.5 mg of ISIS 396443 per mL of solution. In certainembodiments, the concentration of ISIS 396443 in an artificial CSFdiluent is 0.6 mg of ISIS 396443 per mL of solution. In certainembodiments, the concentration of ISIS 396443 in an artificial CSFdiluent is 0.7 mg of ISIS 396443 per mL of solution. In certainembodiments, the concentration of ISIS 396443 in an artificial CSFdiluent is 0.8 mg of ISIS 396443 per mL of solution. In certainembodiments, the concentration of ISIS 396443 in an artificial CSFdiluent is 0.9 mg of ISIS 396443 per mL of solution. In certainembodiments, the concentration of ISIS 396443 in an artificial CSFdiluent is 1.0 mg of ISIS 396443 per mL of solution. In certainembodiments, the concentration of ISIS 396443 in an artificial CSFdiluent is 1.1 mg of ISIS 396443 per mL of solution. In certainembodiments, the concentration of ISIS 396443 in an artificial CSFdiluent is 1.2 mg of ISIS 396443 per mL of solution. In certainembodiments, the concentration of ISIS 396443 in an artificial CSFdiluent is 1.3 mg of ISIS 396443 per mL of solution. In certainembodiments, the concentration of ISIS 396443 in an artificial CSFdiluent is 1.4 mg of ISIS 396443 per mL of solution. In certainembodiments, the concentration of ISIS 396443 in an artificial CSFdiluent is 1.5 mg of ISIS 396443 per mL of solution. In certainembodiments, the concentration of ISIS 396443 in an artificial CSFdiluent is 2.4 mg of ISIS 396443 per mL of solution.

In certain embodiments, the concentration of ISIS 396443 in anartificial CSF diluent is 0.2 mg of ISIS 396443 per mL of solution andthe injection volume is 5.0 mL. In certain embodiments, theconcentration of ISIS 396443 in an artificial CSF diluent is 0.6 mg ofISIS 396443 per mL of solution and the injection volume is 5.0 mL. Incertain embodiments, the concentration of ISIS 396443 in an artificialCSF diluent is 1.2 mg of ISIS 396443 per mL of solution and theinjection volume is 5.0 mL. In certain embodiments, the concentration ofISIS 396443 in an artificial CSF diluent is 1.8 mg of ISIS 396443 per mLof solution and the injection volume is 5.0 mL. In certain embodiments,the concentration of ISIS 396443 in an artificial CSF diluent is 2.0 mgof ISIS 396443 per mL of solution and the injection volume is 5.0 mL. Incertain embodiments, the concentration of ISIS 396443 in an artificialCSF diluent is 2.4 mg of ISIS 396443 per mL of solution and theinjection volume is 4.0 mL. In certain embodiments, the concentration ofISIS 396443 in an artificial CSF diluent is 2.4 mg of ISIS 396443 per mLof solution and the injection volume is 4.3 mL. In certain embodiments,the concentration of ISIS 396443 in an artificial CSF diluent is 2.4 mgof ISIS 396443 per mL of solution and the injection volume is 4.5 mL. Incertain embodiments, the concentration of ISIS 396443 in an artificialCSF diluent is 2.4 mg of ISIS 396443 per mL of solution and theinjection volume is 4.7 mL.

In certain embodiments, the concentration of ISIS 396443 in anartificial CSF diluent is 3 mg of ISIS 396443 per mL of solution and theinjection volume is 4.0 mL. In certain embodiments, the concentration ofISIS 396443 in an artificial CSF diluent is 3 mg of ISIS 396443 per mLof solution and the injection volume is 4.3 mL. In certain embodiments,the concentration of ISIS 396443 in an artificial CSF diluent is 3 mg ofISIS 396443 per mL of solution and the injection volume is 4.5 mL. Incertain embodiments, the concentration of ISIS 396443 in an artificialCSF diluent is 3 mg of ISIS 396443 per mL of solution and the injectionvolume is 4.7 mL.

In certain embodiments, a dose equivalent of ISIS 396443 is calculatedbased on a patient's age or weight. For example, in certain embodimentsa dose may be 6 mg and the dose equivalent may be greater than 6 mg orless than 6 mg.

In certain embodiments, the dose and/or the volume of the injection willbe adjusted based on the patient's age. In certain embodiments, the doseand/or the volume of the injection will be adjusted based on thepatient's CSF volume. In certain embodiments, the dose and/or the volumeof the injection will be adjusted based on the patient's age and/orestimated CSF volume. In certain embodiments, the volume of theinjection is adjusted such that each patient will receive a 6 mg or 9 mgequivalent dose based on CSF volume scaling. (For example, see MatsuzawaJ, Matsui M, Konishi T, Noguchi K, Gur R C, Bilker W, Miyawaki T.Age-related volumetric changes of brain gray and white matter in healthyinfants and children. Cereb Cortex 2001 April; 11(4):335-342, which ishereby incorporated by reference in its entirety). In certainembodiments, the volume of the injection is adjusted such that eachpatient will receive a 12 mg equivalent dose based on CSF volumescaling. (For example, see Matsuzawa J, Matsui M, Konishi T, Noguchi K,Gur R C, Bilker W, Miyawaki T. Age-related volumetric changes of braingray and white matter in healthy infants and children. Cereb Cortex 2001April; 11(4):335-342, which is hereby incorporated by reference in itsentirety).

14. Certain Dose Frequencies

In certain embodiments, multiple doses of ISIS 396443 are administeredto a subject having one or more symptoms associated with SMA. In certainembodiments, two or more doses of ISIS 396443 are administered to asubject having one or more symptoms associated with SMA. In certainembodiments, three or more doses of ISIS 396443 are administered to asubject having one or more symptoms associated with SMA. In certainembodiments, multiple doses of ISIS 396443 are administered to a subjecthaving one or more symptoms associated with SMA. In certain embodiments,multiple doses of ISIS 396443 are administered at the same interval to asubject having one or more symptoms associated with SMA. In certainembodiments, multiple doses of ISIS 396443 are administered at differentintervals to a subject having one or more symptoms associated with SMA.

In certain embodiments, a first dose of ISIS 396443 is administered to asubject having one or more symptoms associated with SMA, a second doseof ISIS 396443 is administered 15 days after the first dose, a thirddose of ISIS 396443 is administered 29 days after the first dose, afourth dose of ISIS 396443 is administered 64 days after the first dose,a fifth dose of ISIS 396443 is administered 183 days after the firstdose, and a sixth dose of ISIS 396443 is administered 302 days after thefirst dose.

In certain embodiments, doses of ISIS 396443 are administered atintervals to a subject having one or more symptoms associated with SMA.In certain embodiments, single doses of ISIS 396443 are administered at15 day intervals to a subject having one or more symptoms associatedwith SMA. In certain embodiments, single doses of ISIS 396443 areadministered at 29 day intervals to a subject having one or moresymptoms associated with SMA. In certain embodiments, single doses ofISIS 396443 are administered at 85 day intervals to a subject having oneor more symptoms associated with SMA.

In certain embodiments a first dose of ISIS 396443 is administered to asubject having one or more symptoms associated with SMA, and a seconddose of ISIS 396443 is administered about 15 days after the first dose.In certain embodiments a first dose of ISIS 396443 is administered to asubject having one or more symptoms associated with SMA, a second doseof ISIS 396443 is administered about 15 days after the first dose, and athird dose of ISIS 396443 is administered about 85 days after the firstdose. In certain embodiments a first dose of ISIS 396443 is administeredto a subject having one or more symptoms associated with SMA, a seconddose of ISIS 396443 is administered about 15 days after the first dose,and a third dose of ISIS 396443 is administered about 29 days after thefirst dose.

In certain embodiments a first dose of ISIS 396443 is administered to asubject having one or more symptoms associated with SMA, a second doseof ISIS 396443 is administered about 15 days after the first dose, athird dose of ISIS 396443 is administered about 29 days after the firstdose, and a fourth dose of ISIS 396443 is administered about 211 daysafter the first dose.

In certain embodiments, single 3 mg doses of ISIS 396443 areadministered at 15 day intervals to a subject having one or moresymptoms associated with SMA. In certain embodiments, single 3 mg dosesof ISIS 396443 are administered at 29 day intervals to a subject havingone or more symptoms associated with SMA. In certain embodiments, single6 mg doses of ISIS 396443 are administered at 85 day intervals to asubject having one or more symptoms associated with SMA.

In certain embodiments, single 9 mg doses of ISIS 396443 areadministered at 29 day intervals to a subject having one or moresymptoms associated with SMA. In certain embodiments, single 9 mg dosesof ISIS 396443 are administered at 85 day intervals to a subject havingone or more symptoms associated with SMA.

In certain embodiments, a first dose of ISIS 396443 is administered to asubject having one or more symptoms associated with SMA and a seconddose of ISIS 396443 is administered 15 days after the first dose. Incertain embodiments, a first dose of ISIS 396443 is administered to asubject having one or more symptoms associated with SMA and a seconddose of ISIS 396443 is administered 29 days after the first dose. Incertain embodiments, a first dose of ISIS 396443 is administered to asubject having one or more symptoms associated with SMA and a seconddose of ISIS 396443 is administered about 1 month after the first dose.In certain embodiments, a first dose of ISIS 396443 is administered to asubject having one or more symptoms associated with SMA and a seconddose of ISIS 396443 is administered about 4 weeks after the first dose.In certain embodiments, a first dose of ISIS 396443 is administered to asubject having one or more symptoms associated with SMA and a seconddose of ISIS 396443 is administered 29 days after the first dose, and athird dose of ISIS 396443 is administered 85 days after the first dose.In certain embodiments, a first dose of ISIS 396443 is administered to asubject having one or more symptoms associated with SMA and a seconddose of ISIS 396443 is administered 85 days after the first dose. Incertain embodiments, a first dose of ISIS 396443 is administered to asubject having one or more symptoms associated with SMA and a seconddose of ISIS 396443 is administered 85 days after the first dose. Incertain embodiments, the first dose and the second dose are the sameamount. In certain embodiments, the first dose and the second dose aredifferent amounts. In certain embodiments, the first, second, and thirddose are the same amount. In certain embodiments, the first, second, andthird dose are different amounts.

In certain embodiments, a first dose of 3 mg of ISIS 396443 isadministered to a subject having one or more symptoms associated withSMA, a second dose of 3 mg of ISIS 396443 is administered 29 days afterthe first dose, and a third dose of 3 mg of ISIS 396443 is administered85 days after the first dose. In certain embodiments, a first dose of 6mg of ISIS 396443 is administered to a subject having one or moresymptoms associated with SMA, a second dose of 6 mg of ISIS 396443 isadministered 29 days after the first dose, and a third dose of 6 mg ofISIS 396443 is administered 85 days after the first dose. In certainembodiments, a first dose of 9 mg of ISIS 396443 is administered to asubject having one or more symptoms associated with SMA, a second doseof 9 mg of ISIS 396443 is administered 29 days after the first dose, anda third dose of 9 mg of ISIS 396443 is administered 85 days after thefirst dose. In certain embodiments, a first dose of 12 mg of ISIS 396443is administered to a subject having one or more symptoms associated withSMA, a second dose of 12 mg of ISIS 396443 is administered 29 days afterthe first dose, and a third dose of 12 mg of ISIS 396443 is administered85 days after the first dose. In certain embodiments, a first dose of 15mg of ISIS 396443 is administered to a subject having one or moresymptoms associated with SMA, a second dose of 15 mg of ISIS 396443 isadministered 29 days after the first dose, and a third dose of 15 mg ofISIS 396443 is administered 85 days after the first dose.

In certain embodiments, a first dose of 3 mg of ISIS 396443 isadministered to a subject having one or more symptoms associated withSMA, a second dose of 3 mg of ISIS 396443 is administered 15 days afterthe first dose, and a third dose of 3 mg of ISIS 396443 is administered85 days after the first dose. In certain embodiments, a first dose of 6mg of ISIS 396443 is administered to a subject having one or moresymptoms associated with SMA, a second dose of 6 mg of ISIS 396443 isadministered 15 days after the first dose, and a third dose of 6 mg ofISIS 396443 is administered 85 days after the first dose. In certainembodiments, a first dose of 9 mg of ISIS 396443 is administered to asubject having one or more symptoms associated with SMA, a second doseof 9 mg of ISIS 396443 is administered 15 days after the first dose, anda third dose of 9 mg of ISIS 396443 is administered 85 days after thefirst dose. In certain embodiments, a first dose of 12 mg of ISIS 396443is administered to a subject having one or more symptoms associated withSMA, a second dose of 12 mg of ISIS 396443 is administered 15 days afterthe first dose, and a third dose of 12 mg of ISIS 396443 is administered85 days after the first dose. In certain embodiments, a first dose of 15mg of ISIS 396443 is administered to a subject having one or moresymptoms associated with SMA, a second dose of 15 mg of ISIS 396443 isadministered 15 days after the first dose, and a third dose of 15 mg ofISIS 396443 is administered 85 days after the first dose.

In certain embodiments, a first dose of 3 mg or equivalent of ISIS396443 is administered to a subject having one or more symptomsassociated with SMA, a second dose of 3 mg or equivalent of ISIS 396443is administered 15 days after the first dose, and a third dose of 3 mgor equivalent of ISIS 396443 is administered 85 days after the firstdose. In certain embodiments, a first dose of 6 mg or equivalent of ISIS396443 is administered to a subject having one or more symptomsassociated with SMA, a second dose of 6 mg or equivalent of ISIS 396443is administered 15 days after the first dose, and a third dose of 6 mgor equivalent of ISIS 396443 is administered 85 days after the firstdose. In certain embodiments, a first dose of 9 mg or equivalent of ISIS396443 is administered to a subject having one or more symptomsassociated with SMA, a second dose of 9 mg or equivalent of ISIS 396443is administered 15 days after the first dose, and a third dose of 9 mgor equivalent of ISIS 396443 is administered 85 days after the firstdose. In certain embodiments, a first dose of 12 mg or equivalent ofISIS 396443 is administered to a subject having one or more symptomsassociated with SMA, a second dose of 12 mg or equivalent of ISIS 396443is administered 15 days after the first dose, and a third dose of 12 mgor equivalent of ISIS 396443 is administered 85 days after the firstdose. In certain embodiments, a first dose of 15 mg or equivalent ofISIS 396443 is administered to a subject having one or more symptomsassociated with SMA, a second dose of 15 mg or equivalent of ISIS 396443is administered 15 days after the first dose, and a third dose of 15 mgor equivalent of ISIS 396443 is administered 85 days after the firstdose.

In certain embodiments, a first dose of 3 mg of ISIS 396443 isadministered to a subject having one or more symptoms associated withSMA, and a second dose of 3 mg of ISIS 396443 is administered six monthsafter the first dose, and a third dose of 3 mg of ISIS 396443 isadministered 12 months after the first dose. In certain embodiments, afirst dose of 6 mg of ISIS 396443 is administered to a subject havingone or more symptoms associated with SMA, a second dose of 6 mg of ISIS396443 is administered six months after the first dose, and a third doseof 6 mg of ISIS 396443 is administered 12 months after the first dose.In certain embodiments, a first dose of 9 mg of ISIS 396443 isadministered to a subject having one or more symptoms associated withSMA, a second dose of 9 mg of ISIS 396443 is administered six monthsafter the first dose, and a third dose of 9 mg of ISIS 396443 isadministered 12 months after the first dose. In certain embodiments, afirst dose of 12 mg of ISIS 396443 is administered to a subject havingone or more symptoms associated with SMA, a second dose of 12 mg of ISIS396443 is administered six months after the first dose, and a third doseof 12 mg of ISIS 396443 is administered 12 months after the first dose.In certain embodiments, a first dose of 15 mg of ISIS 396443 isadministered to a subject having one or more symptoms associated withSMA, a second dose of 15 mg of ISIS 396443 is administered six monthsafter the first dose, and a third dose of 15 mg of ISIS 396443 isadministered 12 months after the first dose.

In certain embodiments, a first dose of 3 mg or equivalent of ISIS396443 is administered to a subject having one or more symptomsassociated with SMA, and a second dose of 3 mg or equivalent of ISIS396443 is administered 12 months after the first dose. In certainembodiments, a first dose of 6 mg or equivalent of ISIS 396443 isadministered to a subject having one or more symptoms associated withSMA, and a second dose of 6 mg or equivalent of ISIS 396443 isadministered 12 months after the first dose. In certain embodiments, afirst dose of 9 mg or equivalent of ISIS 396443 is administered to asubject having one or more symptoms associated with SMA, and a seconddose of 9 mg or equivalent of ISIS 396443 is administered 12 monthsafter the first dose. In certain embodiments, a first dose of 12 mg orequivalent of ISIS 396443 is administered to a subject having one ormore symptoms associated with SMA, and a second dose of 12 mg orequivalent of ISIS 396443 is administered 12 months after the firstdose. In certain embodiments, a first dose of 15 mg or equivalent ofISIS 396443 is administered to a subject having one or more symptomsassociated with SMA, and a second dose of 15 mg or equivalent of ISIS396443 is administered 12 months after the first dose.

In certain embodiments, a first dose of 3 mg or equivalent of ISIS396443 is administered to a subject having one or more symptomsassociated with SMA, and a second dose of 3 mg or equivalent of ISIS396443 is administered 13 months after the first dose. In certainembodiments, a first dose of 6 mg or equivalent of ISIS 396443 isadministered to a subject having one or more symptoms associated withSMA, and a second dose of 6 mg or equivalent of ISIS 396443 isadministered 13 months after the first dose. In certain embodiments, afirst dose of 9 mg or equivalent of ISIS 396443 is administered to asubject having one or more symptoms associated with SMA, and a seconddose of 9 mg or equivalent of ISIS 396443 is administered 13 monthsafter the first dose. In certain embodiments, a first dose of 12 mg orequivalent of ISIS 396443 is administered to a subject having one ormore symptoms associated with SMA, and a second dose of 12 mg orequivalent of ISIS 396443 is administered 13 months after the firstdose. In certain embodiments, a first dose of 15 mg or equivalent ofISIS 396443 is administered to a subject having one or more symptomsassociated with SMA, and a second dose of 15 mg or equivalent of ISIS396443 is administered 13 months after the first dose.

In certain embodiments, a first dose of 3 mg or equivalent of ISIS396443 is administered to a subject having one or more symptomsassociated with SMA, and a second dose of 3 mg or equivalent of ISIS396443 is administered 14 months after the first dose. In certainembodiments, a first dose of 6 mg or equivalent of ISIS 396443 isadministered to a subject having one or more symptoms associated withSMA, and a second dose of 6 mg or equivalent of ISIS 396443 isadministered 14 months after the first dose. In certain embodiments, afirst dose of 9 mg or equivalent of ISIS 396443 is administered to asubject having one or more symptoms associated with SMA, and a seconddose of 9 mg or equivalent of ISIS 396443 is administered 14 monthsafter the first dose. In certain embodiments, a first dose of 12 mg orequivalent of ISIS 396443 is administered to a subject having one ormore symptoms associated with SMA, and a second dose of 12 mg orequivalent of ISIS 396443 is administered 14 months after the firstdose. In certain embodiments, a first dose of 15 mg or equivalent ofISIS 396443 is administered to a subject having one or more symptomsassociated with SMA, and a second dose of 15 mg or equivalent of ISIS396443 is administered 14 months after the first dose.

In certain embodiments, a first dose of 3 mg or equivalent of ISIS396443 is administered to a subject having one or more symptomsassociated with SMA, and a second dose of 3 mg or equivalent of ISIS396443 is administered 15 months after the first dose. In certainembodiments, a first dose of 6 mg or equivalent of ISIS 396443 isadministered to a subject having one or more symptoms associated withSMA, and a second dose of 6 mg or equivalent of ISIS 396443 isadministered 15 months after the first dose. In certain embodiments, afirst dose of 9 mg or equivalent of ISIS 396443 is administered to asubject having one or more symptoms associated with SMA, and a seconddose of 9 mg or equivalent of ISIS 396443 is administered 15 monthsafter the first dose. In certain embodiments, a first dose of 12 mg orequivalent of ISIS 396443 is administered to a subject having one ormore symptoms associated with SMA, and a second dose of 12 mg orequivalent of ISIS 396443 is administered 15 months after the firstdose. In certain embodiments, a first dose of 15 mg or equivalent ofISIS 396443 is administered to a subject having one or more symptomsassociated with SMA, and a second dose of 15 mg or equivalent of ISIS396443 is administered 15 months after the first dose.

In certain embodiments, a first dose of 3 mg or equivalent of ISIS396443 is administered to a subject having one or more symptomsassociated with SMA, and subsequent doses of 3 mg or equivalent of ISIS396443 are administered at 6 month intervals thereafter. In certainembodiments, a first dose of 6 mg or equivalent of ISIS 396443 isadministered to a subject having one or more symptoms associated withSMA, and subsequent doses of 6 mg or equivalent of ISIS 396443 areadministered at 6 month intervals thereafter. In certain embodiments, afirst dose of 9 mg or equivalent of ISIS 396443 is administered to asubject having one or more symptoms associated with SMA, and subsequentdoses of 9 mg or equivalent of ISIS 396443 are administered at 6 monthintervals thereafter. In certain embodiments, a first dose of 12 mg orequivalent of ISIS 396443 is administered to a subject having one ormore symptoms associated with SMA, and subsequent doses of 12 mg orequivalent of ISIS 396443 are administered at 6 month intervalsthereafter. In certain embodiments, a first dose of 15 mg or equivalentof ISIS 396443 is administered to a subject having one or more symptomsassociated with SMA, and subsequent doses of 15 mg or equivalent of ISIS396443 are administered at 6 month intervals thereafter.

In certain embodiments, a first dose of 3 mg or equivalent of ISIS396443 is administered to a subject having one or more symptomsassociated with SMA, and subsequent doses of 3 mg or equivalent of ISIS396443 are administered at 12 month intervals thereafter. In certainembodiments, a first dose of 6 mg or equivalent of ISIS 396443 isadministered to a subject having one or more symptoms associated withSMA, and subsequent doses of 6 mg or equivalent of ISIS 396443 areadministered at 12 month intervals thereafter. In certain embodiments, afirst dose of 9 mg or equivalent of ISIS 396443 is administered to asubject having one or more symptoms associated with SMA, and subsequentdoses of 9 mg or equivalent of ISIS 396443 are administered at 12 monthintervals thereafter. In certain embodiments, a first dose of 12 mg orequivalent of ISIS 396443 is administered to a subject having one ormore symptoms associated with SMA, and subsequent doses of 12 mg orequivalent of ISIS 396443 are administered at 12 month intervalsthereafter. In certain embodiments, a first dose of 15 mg or equivalentof ISIS 396443 is administered to a subject having one or more symptomsassociated with SMA, and subsequent doses of 15 mg or equivalent of ISIS396443 are administered at 12 month intervals thereafter.

In certain embodiments, a first dose of 3 mg or equivalent of ISIS396443 is administered to a subject having one or more symptomsassociated with SMA, and subsequent doses of 3 mg or equivalent of ISIS396443 are administered at 13 month intervals thereafter. In certainembodiments, a first dose of 6 mg or equivalent of ISIS 396443 isadministered to a subject having one or more symptoms associated withSMA, and subsequent doses of 6 mg or equivalent of ISIS 396443 areadministered at 13 month intervals thereafter. In certain embodiments, afirst dose of 9 mg or equivalent of ISIS 396443 is administered to asubject having one or more symptoms associated with SMA, and subsequentdoses of 9 mg or equivalent of ISIS 396443 are administered at 13 monthintervals thereafter. In certain embodiments, a first dose of 12 mg orequivalent of ISIS 396443 is administered to a subject having one ormore symptoms associated with SMA, and subsequent doses of 12 mg orequivalent of ISIS 396443 are administered at 13 month intervalsthereafter. In certain embodiments, a first dose of 15 mg or equivalentof ISIS 396443 is administered to a subject having one or more symptomsassociated with SMA, and subsequent doses of 15 mg or equivalent of ISIS396443 are administered at 13 month intervals thereafter.

In certain embodiments, a first dose of 3 mg or equivalent of ISIS396443 is administered to a subject having one or more symptomsassociated with SMA, and subsequent doses of 3 mg or equivalent of ISIS396443 are administered at 14 month intervals thereafter. In certainembodiments, a first dose of 6 mg or equivalent of ISIS 396443 isadministered to a subject having one or more symptoms associated withSMA, and subsequent doses of 6 mg or equivalent of ISIS 396443 areadministered at 14 month intervals thereafter. In certain embodiments, afirst dose of 9 mg or equivalent of ISIS 396443 is administered to asubject having one or more symptoms associated with SMA, and subsequentdoses of 9 mg or equivalent of ISIS 396443 are administered at 14 monthintervals thereafter. In certain embodiments, a first dose of 12 mg orequivalent of ISIS 396443 is administered to a subject having one ormore symptoms associated with SMA, and subsequent doses of 12 mg orequivalent of ISIS 396443 are administered at 14 month intervalsthereafter. In certain embodiments, a first dose of 15 mg or equivalentof ISIS 396443 is administered to a subject having one or more symptomsassociated with SMA, and subsequent doses of 15 mg or equivalent of ISIS396443 are administered at 14 month intervals thereafter.

In certain embodiments, a first dose of 3 mg or equivalent of ISIS396443 is administered to a subject having one or more symptomsassociated with SMA, and subsequent doses of 3 mg or equivalent of ISIS396443 are administered at 15 month intervals thereafter. In certainembodiments, a first dose of 6 mg or equivalent of ISIS 396443 isadministered to a subject having one or more symptoms associated withSMA, and subsequent doses of 6 mg or equivalent of ISIS 396443 areadministered at 15 month intervals thereafter. In certain embodiments, afirst dose of 9 mg or equivalent of ISIS 396443 is administered to asubject having one or more symptoms associated with SMA, and subsequentdoses of 9 mg or equivalent of ISIS 396443 are administered at 15 monthintervals thereafter. In certain embodiments, a first dose of 12 mg orequivalent of ISIS 396443 is administered to a subject having one ormore symptoms associated with SMA, and subsequent doses of 12 mg orequivalent of ISIS 396443 are administered at 15 month intervalsthereafter. In certain embodiments, a first dose of 15 mg or equivalentof ISIS 396443 is administered to a subject having one or more symptomsassociated with SMA, and subsequent doses of 15 mg or equivalent of ISIS396443 are administered at 15 month intervals thereafter.

In certain embodiments, a first dose of 3 mg of ISIS 396443 isadministered to a subject having one or more symptoms associated withSMA, a second dose of 3 mg of ISIS 396443 is administered 15 days afterthe first dose, a third dose of 3 mg of ISIS 396443 is administered 29days after the first dose, and a fourth dose of 3 mg of ISIS 396443 isadministered 211 days after the first dose. In certain embodiments, afirst dose of 6 mg of ISIS 396443 is administered to a subject havingone or more symptoms associated with SMA, a second dose of 6 mg of ISIS396443 is administered 15 days after the first dose, a third dose of 6mg of ISIS 396443 is administered 29 days after the first dose, and afourth dose of 6 mg of ISIS 396443 is administered 211 days after thefirst dose. In certain embodiments, a first dose of 9 mg of ISIS 396443is administered to a subject having one or more symptoms associated withSMA, a second dose of 9 mg of ISIS 396443 is administered 15 days afterthe first dose, a third dose of 9 mg of ISIS 396443 is administered 29days after the first dose, and a fourth dose of 9 mg of ISIS 396443 isadministered 211 days after the first dose. In certain embodiments, afirst dose of 12 mg of ISIS 396443 is administered to a subject havingone or more symptoms associated with SMA, a second dose of 12 mg of ISIS396443 is administered 15 days after the first dose, a third dose of 12mg of ISIS 396443 is administered 29 days after the first dose, and afourth dose of 12 mg of ISIS 396443 is administered 211 days after thefirst dose. In certain embodiments, a first dose of 15 mg of ISIS 396443is administered to a subject having one or more symptoms associated withSMA, a second dose of 15 mg of ISIS 396443 is administered 15 days afterthe first dose, a third dose of 15 mg of ISIS 396443 is administered 29days after the first dose, and a fourth dose of 15 mg of ISIS 396443 isadministered 211 days after the first dose.

In certain embodiments, a first dose of 3 mg of ISIS 396443 isadministered to a subject having one or more symptoms associated withSMA, a second dose of 3 mg of ISIS 396443 is administered 15 days afterthe first dose, a third dose of 3 mg of ISIS 396443 is administered 29days after the first dose, a fourth dose of 3 mg of ISIS 396443 isadministered 64 days after the first dose, a fifth dose of 3 mg of ISIS396443 is administered 183 days after the first dose, and a sixth doseof 3 mg of ISIS 396443 is administered 302 days after the first dose.

In certain embodiments, a first dose of 6 mg of ISIS 396443 isadministered to a subject having one or more symptoms associated withSMA, a second dose of 6 mg of ISIS 396443 is administered 15 days afterthe first dose, a third dose of 6 mg of ISIS 396443 is administered 29days after the first dose, a fourth dose of 6 mg of ISIS 396443 isadministered 64 days after the first dose, a fifth dose of 6 mg of ISIS396443 is administered 183 days after the first dose, and a sixth doseof 6 mg of ISIS 396443 is administered 302 days after the first dose.

In certain embodiments, a first dose of 9 mg of ISIS 396443 isadministered to a subject having one or more symptoms associated withSMA, a second dose of 9 mg of ISIS 396443 is administered 15 days afterthe first dose, a third dose of 9 mg of ISIS 396443 is administered 29days after the first dose, a fourth dose of 9 mg of ISIS 396443 isadministered 64 days after the first dose, a fifth dose of 9 mg of ISIS396443 is administered 183 days after the first dose, and a sixth doseof 9 mg of ISIS 396443 is administered 302 days after the first dose.

In certain embodiments, a first dose of 12 mg of ISIS 396443 isadministered to a subject having one or more symptoms associated withSMA, a second dose of 12 mg of ISIS 396443 is administered 15 days afterthe first dose, a third dose of 12 mg of ISIS 396443 is administered 29days after the first dose, a fourth dose of 12 mg of ISIS 396443 isadministered 64 days after the first dose, a fifth dose of 12 mg of ISIS396443 is administered 183 days after the first dose, and a sixth doseof 12 mg of ISIS 396443 is administered 302 days after the first dose.

In certain embodiments, a first dose of 15 mg of ISIS 396443 isadministered to a subject having one or more symptoms associated withSMA, a second dose of 15 mg of ISIS 396443 is administered 15 days afterthe first dose, a third dose of 15 mg of ISIS 396443 is administered 29days after the first dose, a fourth dose of 15 mg of ISIS 396443 isadministered 64 days after the first dose, a fifth dose of 15 mg of ISIS396443 is administered 183 days after the first dose, and a sixth doseof 15 mg of ISIS 396443 is administered 302 days after the first dose.

In certain embodiments, a first dose of 18 mg of ISIS 396443 isadministered to a subject having one or more symptoms associated withSMA, a second dose of 18 mg of ISIS 396443 is administered 15 days afterthe first dose, a third dose of 18 mg of ISIS 396443 is administered 29days after the first dose, a fourth dose of 18 mg of ISIS 396443 isadministered 64 days after the first dose, a fifth dose of 18 mg of ISIS396443 is administered 183 days after the first dose, and a sixth doseof 18 mg of ISIS 396443 is administered 302 days after the first dose.

In certain embodiments, a first dose of 12 mg of ISIS 396443 isadministered to a subject having one or more symptoms associated withSMA, a second dose is administered 12-18 days after the first dose, athird dose is administered 25-35 days after the first dose, a fourthdose is administered 60-70 days after the first dose, a fifth dose isadministered 178-188 days after the first dose, a sixth dose isadministered 298-308 days after the first dose is administered, and eachsubsequent dose thereafter is administered at six month intervals.

In certain embodiments, a first dose of 12 mg equivalent of ISIS 396443is administered to a subject having one or more symptoms associated withType I SMA, a second dose is administered 12-18 days after the firstdose, a third dose is administered 25-35 days after the first dose, afourth dose is administered 60-70 days after the first dose, a fifthdose is administered 178-188 days after the first dose, a sixth dose isadministered 298-308 days after the first dose is administered, and eachsubsequent dose thereafter is administered at six month intervals.

Proposed dose frequency is approximate, for example, in certainembodiments if the proposed dose frequency is a dose at day 1 and asecond dose at day 29, an SMA patient may receive a second dose 25, 26,27, 28, 29, 30, 31, 32, 33, or 34 days after receipt of the first dose.In certain embodiments, if the proposed dose frequency is a dose at day1 and a second dose at day 15, an SMA patient may receive a second dose10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 days after receipt of thefirst dose. In certain embodiments, if the proposed dose frequency is adose at day 1 and a second dose at day 85, an SMA patient may receive asecond dose 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, or 90 days afterreceipt of the first dose.

In certain embodiments, the dose and/or the volume of the injection willbe adjusted based on the patient's age. In certain embodiments, the doseand/or the volume of the injection will be adjusted based on thepatient's CSF volume. In certain embodiments, the dose and/or the volumeof the injection will be adjusted based on the patient's age and/orestimated CSF volume. In certain embodiments, the volume of theinjection is adjusted such that each patient will receive a 12 mgequivalent dose based on CSF volume scaling. (For example, see MatsuzawaJ, Matsui M, Konishi T, Noguchi K, Gur R C, Bilker W, Miyawaki T.Age-related volumetric changes of brain gray and white matter in healthyinfants and children. Cereb Cortex 2001 April; 11(4):335-342, which ishereby incorporated by reference in its entirety). In certainembodiments, the volume of the injection is adjusted such that eachpatient will receive a 12 mg equivalent dose based on CSF volumescaling. (For example, see Matsuzawa J, Matsui M, Konishi T, Noguchi K,Gur R C, Bilker W, Miyawaki T. Age-related volumetric changes of braingray and white matter in healthy infants and children. Cereb Cortex 2001April; 11(4):335-342, which is hereby incorporated by reference in itsentirety).

15. Co-Administration

In certain embodiments, pharmaceutical compositions of the presentinvention are co-administered with at least one other pharmaceuticalcomposition for treating SMA and/or for treating one or more symptomassociated with SMA. In certain embodiments, such other pharmaceuticalcomposition is selected from trichostatin-A, valproic acid, riluzole,hydroxyurea, and a butyrate or butyrate derivative. In certainembodiments, pharmaceutical compositions of the present invention areco-administered with trichostatin A. In certain embodiments,pharmaceutical compositions of the present invention are co-administeredwith a derivative of quinazoline, for example as described in Thurmond,et al., J. Med Chem. 2008, 51, 449-469. In certain embodiments, apharmaceutical composition of the present invention and at least oneother pharmaceutical composition are co-administered at the same time.In certain embodiments, a pharmaceutical composition of the presentinvention and at least one other pharmaceutical composition areco-administered at different times.

In certain embodiments, pharmaceutical compositions of the presentinvention are co-administered with a gene therapy agent. In certain suchembodiments, the gene therapy agent is administered to the CSF and thepharmaceutical composition of the present invention is administeredsystemically. In certain such embodiments, the gene therapy agent isadministered to the CSF and the pharmaceutical composition of thepresent invention is administered to the CSF and systemically. Incertain embodiments, a pharmaceutical composition of the presentinvention and a gene therapy agent are co-administered at the same time.In certain embodiments, a pharmaceutical composition of the presentinvention and a gene therapy agent are co-administered at differenttimes. Certain gene therapy approaches to SMA treatment have beenreported (e.g., Coady et al., PLoS ONE 2008 3(10): e3468; Passini etal., J Clin Invest 2010 Apr. 1, 120(4): 1253-64).

In certain embodiments, pharmaceutical compositions of the presentinvention are co-administered with at least one other therapy for SMA.In certain embodiments, such other therapy for SMA is surgery. Incertain embodiments, such other therapy is physical therapy, including,but not limited to exercises designed to strengthen muscles necessaryfor breathing, such as cough therapy. In certain embodiments, othertherapy is a physical intervention, such as a feeding tube or device forassisted breathing.

In certain embodiments, pharmaceutical compositions of the presentinvention are co-administered with one or more other pharmaceuticalcompositions that reduce an undesired side-effect of the pharmaceuticalcompositions of the present invention.

16. Phenotypic Effects

In certain embodiments, administration of at least one pharmaceuticalcomposition of the present invention results in a phenotypic change inthe subject. In certain embodiments, such phenotypic changes include,but are not limited to: increased absolute amount of SMN mRNA thatincludes exon 7; increase in the ratio SMN mRNA that includes exon 7 toSMN mRNA lacking exon 7; increased absolute amount of SMN protein thatincludes exon 7; increase in the ratio SMN protein that includes exon 7to SMN protein lacking exon 7; improved muscle strength, improvedelectrical activity in at least one muscle; improved respiration; weightgain; and survival. In certain embodiments, at least one phenotypicchange is detected in a motoneuron of the subject. In certainembodiments, administration of at least one pharmaceutical compositionof the present invention results in a subject being able to sit-up, tostand, and/or to walk. In certain embodiments, administration of atleast one pharmaceutical composition of the present invention results ina subject being able to eat, drink, and/or breathe without assistance.In certain embodiments, efficacy of treatment is assessed byelectrophysiological assessment of muscle. In certain embodiments,administration of a pharmaceutical composition of the present inventionimproves at least one symptom of SMA and has little or no inflammatoryeffect. In certain such embodiment, absence of inflammatory effect isdetermined by the absence of significant increase in Aif1 levels upontreatment.

In certain embodiments, administration of at least one pharmaceuticalcomposition of the present invention delays the onset of at least onesymptom of SMA. In certain embodiments, administration of at least onepharmaceutical composition of the present invention slows theprogression of at least one symptom of SMA. In certain embodiments,administration of at least one pharmaceutical composition of the presentinvention reduces the severity of at least one symptom of SMA.

In certain embodiments, administration of at least one pharmaceuticalcomposition of the present disclosure to a subject having SMA results inthe subject improving his or her Hammersmith Functional MotorScale-Expanded (HFMSE). The HFMSE is a reliable and validated tool usedto assess motor function in children with SMA. In certain embodiments,the HFMSE is used to assess responses on 33 motor function tasks, whereeach task is scored on a scale from 0 to 2. In certain embodiments,administration of at least one pharmaceutical composition of the presentdisclosure to a subject having SMA results in the subject improving hisor her Pediatric Quality of Life Inventory (PedsQL™) Measurement 4.0Generic Core Scales. In certain embodiments, administration of at leastone pharmaceutical composition of the present disclosure to a subjecthaving SMA results in the subject improving his or her Pediatric Qualityof Life Inventory 3.0 Neuromuscular Modules. In certain embodiments,administration of at least one pharmaceutical composition of the presentdisclosure to a subject having SMA results in the subject improving hisor her health-related quality of life. In certain embodiments,administration of at least one pharmaceutical composition of the presentdisclosure to a subject having SMA results in the subject improving hisor her Compound Muscle Action Potential (CMAP). In certain embodiments,administration of at least one pharmaceutical composition of the presentdisclosure to a subject having SMA results in the subject improving hisor her Motor Unit Number Estimation (MUNE). CMAP and MUNE areelectrophysiological techniques that can be used to determine theapproximate number of motor neurons in a muscle or group of muscles.MUNE methods also provide a means of measuring motor unit size, enablingtracking of the number of motor units and the compensatory phenomenon ofcollateral reinnervation. CMAP and MUNE are well validated methods fortracking disease progression in neuromuscular disorders such as spinalmuscular atrophy and amyotrophic lateral sclerosis.

In certain embodiments, administration of at least one pharmaceuticalcomposition of the present invention results in an undesiredside-effect. In certain embodiments, a treatment regimen is identifiedthat results in desired amelioration of symptoms while avoidingundesired side-effects.

17. Dosage Units

In certain embodiments pharmaceutical compositions of the presentinvention are prepared as dosage units for administration. Certain suchdosage units are at concentrations selected from 0.01 mg to 100 mg. Incertain such embodiments, a pharmaceutical composition of the presentinvention comprises a dose of antisense compound selected from 0.01 mg,0.1 mg, 0.5 mg, 1 mg, 5 mg, 10 mg, 20 mg, 25 mg, 50 mg, 75 mg, 100 mg,150 mg, and 200 mg. In certain embodiments, a pharmaceutical compositionis comprises a dose of oligonucleotide selected from 0.1 mg, 0.5 mg, 1mg, 5 mg, 10 mg, 25 mg, and 50 mg.

18. Kits

In certain embodiments, the present disclosure provides kits comprisingat least one pharmaceutical composition. In certain embodiments, suchkits further comprise a means of delivery, for example a syringe orinfusion pump.

In certain embodiments, the present disclosure provides kits comprisinga means for measuring the amount of SMN protein in a sample of CSF. Incertain embodiments, the present disclosure provides kits comprising oneor more antibodies and provides a means for measuring the amount of SMNprotein in a sample of CSF.

In certain embodiments, the present disclosure provides kits comprisinga capture antibody and a detection antibody. In certain embodiments, thecapture antibody recognizes an N-terminal epitope of the SMN2 protein.In certain embodiments, the capture antibody specifically binds to apolypeptide comprising the amino acid sequence: gggvpeq (SEQ ID NO: 25).In certain embodiments, the capture antibody specifically binds to apolypeptide comprising the amino acid sequence: mamssggsgg gvpeqedsvlfrr (SEQ ID NO: 26). In certain embodiments, the capture antibody isMillipore antibody MABE230. In certain embodiments, the detectionantibody specifically binds to a polypeptide comprising the amino acidsequence: DNIKPKS (SEQ ID NO: 27). In certain embodiments, the detectionantibody specifically binds to a polypeptide comprising the amino acidsequence: srspgnks dnikpksapw nsflp (SEQ ID NO: 28). In certainembodiments, the detection antibody is ProteinTech antibody #60154-1-Ig.

Nonlimiting Disclosure and Incorporation by Reference

While certain compounds, compositions and methods described herein havebeen described with specificity in accordance with certain embodiments,the following examples serve only to illustrate the compounds describedherein and are not intended to limit the same. Each of the references,GenBank accession numbers, and the like recited herein is herebyincorporated by reference in its entirety.

Although the sequence listing accompanying this filing identifies eachsequence as either “RNA” or “DNA” as required, in reality, thosesequences may be modified with any combination of chemicalmodifications. One of skill in the art will readily appreciate that suchdesignation as “RNA” or “DNA” to describe modified oligonucleotides is,in certain instances, arbitrary. For example, an oligonucleotidecomprising a nucleoside comprising a 2′-OH sugar moiety and a thyminebase could be described as a DNA having a modified sugar (2′-OH for thenatural 2′-H of DNA) or as an RNA having a modified base (thymine(methylated uracil) for natural uracil of RNA).

Accordingly, nucleic acid sequences provided herein, including, but notlimited to those in the sequence listing, are intended to encompassnucleic acids containing any combination of natural or modified RNAand/or DNA, including, but not limited to such nucleic acids havingmodified nucleobases. By way of further example and without limitation,an oligomeric compound having the nucleobase sequence “ATCGATCG”encompasses any oligomeric compounds having such nucleobase sequence,whether modified or unmodified, including, but not limited to, suchcompounds comprising RNA bases, such as those having sequence “AUCGAUCG”and those having some DNA bases and some RNA bases such as “AUCGATCG”and oligomeric compounds having other modified bases, such as“AT^(me)CGAUCG,” wherein meC indicates a cytosine base comprising amethyl group at the 5-position.

EXAMPLES Non-Limiting Disclosure and Incorporation by Reference

While certain compounds, compositions and methods described herein havebeen described with specificity in accordance with certain embodiments,the following examples serve only to illustrate the compounds describedherein and are not intended to limit the same. Each of the referencesrecited in the present application is incorporated herein by referencein its entirety.

Example 1—Antisense Compounds Targeting SMN2

The following oligonucleotides were synthesized using standardtechniques previously reported.

Reference # Sequence Length Chemistry SEQ ID NO ISIS396443TCACTTTCATAATGCTGG 18 Full 2′-MOE; full PS 1 ISIS396449 TTTCATAATGCTGGC15 Full 2′-MOE; full PS 2 PS = phosphorothioate internucleoside linkagesAll C residues are 5-methylcytosines.

Example 2: Selection of Antibodies

A series of monoclonal SMN antibodies were evaluated for binding toHis-tagged recombinant human SMN protein (ProteinTech, catalog #ag14333) using a Bio-Layer Interferometry system (BLItz, Fortebio Inc.,Menlo Park, Calif.). The antibodies tested were BD Biosciences anti-SMN(catalog #610647), Millipore anti-SMN2 (catalog # MABE230), ProteinTechanti-SMN2 (catalog #60154-1-Ig), and ProteinTech anti-SMN2 (catalog#60154-2-Ig). A previously tested antibody, Enzo anti-SMN1 (catalog #ADI-NBA-202-200), was used as a positive control. The His-taggedrecombinant human SMN protein was added to the BLItz instrument andimmobilized to the BLI biosensor tip surface. In each run, a differentantibody was added to the instrument and binding was measured over time.The resulting rate and dissociation constants (k_(a), k_(d), and K_(D))were calculated, and the results are listed in Table 1. The results showthat the ProteinTech antibody #60154-1-Ig and Millipore antibody MABE230had the lowest K_(D) values.

TABLE 1 Bio-Layer Interferometry Antibody k_(a) (1/M · s) k_(d) (1/s)K_(D) (M) Enzo ADI-NBA-202- 1.23 × 10⁴ <1 × 10⁻⁷ <1 × 10⁻¹⁰ 200 BD610647 6.37 × 10⁵ 1.09 × 10²   1.71 × 10⁻⁴   MABE230 1.05 × 10⁵ <1 ×10⁻⁷ <1 × 10⁻¹² PT 60154-1-Ig 1.18 × 10⁵ <1 × 10⁻⁷ <1 × 10⁻¹² PT60154-2-Ig 8.84 × 10² <1 × 10⁻⁷ <1 × 10⁻⁹ 

Example 3: Selection of Antibody Orientation

The MABE230 and PT 60154-1-Ig antibodies from Example 1 were selectedfor use in an SMN detection assay using the Erenna Immunoassay System(Singulex, Alameda, Calif.). In order to determine the antibodyorientation to be used, two sets of conditions were tested. In the firstset of conditions tested, MABE230 was used as the capture antibody andPT 60154-1-Ig was used as the detection antibody (Table 2). In thesecond set of conditions tested, PT 60154-1-Ig was used as the captureantibody and MABE230 was used as the detection antibody (Table 3). Ineach case, the capture antibody was labeled with a chemical handle tofacilitate binding to magnetic microparticles (MPs, Singulex), and thedetection antibody was labeled with a fluorophore prior to use in theassay.

MPs coated with a ligand that binds the capture antibody label weremixed with 12.5 or 25 μg of capture antibody per mg of MPs, then dilutedto 50 or 100 μg/mL in assay buffer containing Tris buffer, BSA, 0.25%surfactant and a comprehensive blocking cocktail (Singulex). His-taggedrecombinant human SMN protein (ProteinTech, catalog # ag14333) wasdiluted to 2 or 10 pg/mL in standard diluent comprising Tris buffer anda high concentration of BSA (Singulex). 100 μL of the captureantibody-MP mixture and either 100 μL of the diluted human SMNrecombinant protein or 100 μL of standard diluent were added to eachwell of a 96-well plate and incubated two hours at 25° C. in a Jitterbugshaker (Boekel Scientific, Feasterville, Pa.) set to speed 5. In orderto remove unbound capture antibody, the MPs were then retained via amagnetic bed and washed once with buffered saline solution containingsurfactant (wash buffer, Singulex) using a Hydroflex 96-well platewasher (Tecan, Switzerland). The detection antibody was diluted to 50,100, 500, or 1,000 ng/mL in assay buffer, filtered through a 0.2 μmfilter (catalog #4187, Pall, Port Washington, N.Y.), and 20 μL of thediluted detection antibody was added to each well of the 96-well plate.The plate was incubated one hour at 25° C. in a Jitterbug shaker set tospeed 5. In order to remove unbound detection antibody, the MPs werethen retained via a magnetic bed and washed four times with wash bufferusing the Hydroflex plate washer. In order to eliminate fluorescentsignal from non-specific binding of the detection antibody to the96-well plate, the samples were then transferred to a new 96-well plate,and the remaining buffer was aspirated. 10 μL of Elution Buffer B(Singulex) was then added to each well, incubated at least five minutesat 25° C. in a Jitterbug shaker set to speed 5. While the MPs wereretained via a magnetic bed, the elution mixture containing thedetection antibody was transferred to a 384-well plate containing 10 μLof Buffer D (neutralization buffer, Singulex) per well. The amount ofdetection antibody present in each well was determined via singlemolecule counting using the Erenna System. Each well was read on theErenna System for 60 seconds.

In Tables 2 and 3, “Cap Ab” indicates capture antibody, “Det Ab”indicates detection antibody, “n” indicates the number of replicate runscompleted, “DE” indicates average detected events for each set ofreplicates, “SD” indicates standard deviation, “CV %” indicates thepercent coefficient of variation, and “LoD” indicates the limit ofdetection. The slope refers to the slope of the line generated by thetwo SMN analyte concentration points tested for each condition (0 and 2pg/mL or 0 and 10 pg/mL). LoD was calculated by multiplying the standarddeviation of the background signal by two and dividing it by the slope.Optimal conditions are those in which background signal is low and DEsignal is high (giving a high slope) and in which LoD is low. Thebackground signal is the average DE at 0 pg/mL SMN protein for each setof conditions tested.

TABLE 2 Erenna assay with MABE230 as capture antibody and PT 60154-4-Igas detection antibody MPs Cap [SMN] DE LoD (μg/ Det Ab Ab/MP (pg/ DE CV(pg/ well) (ng/mL) (μg/mg) mL) n DE SD % Slope mL) 10 1000 25 2 3 2668174 7 1272 0.023 0 3 125 15 12 12.5 2 3 2919 82 3 1413 0.021 0 3 94 1515 500 25 2 3 2396 234 10 1145 0.006 0 3 106 4 3 12.5 2 3 2116 121 61035 0.023 0 3 46 12 26 100 25 2 3 1128 56 5 525 0.043 0 3 78 11 15 12.52 3 1047 181 17 510 0.053 0 3 28 14 48 50 25 2 3 776 28 4 361 0.012 0 255 2 4 12.5 2 3 681 7 1 329 0.017 0 2 22 3 13 5 1000 25 2 3 2185 349 161052 0.099 0 3 81 52 64 12.5 2 3 2589 276 11 1274 0.013 0 3 41 8 20 50025 2 3 1931 36 2 942 0.003 0 3 47 2 3 12.5 2 3 1952 128 7 967 0.007 0 319 4 19 100 25 2 3 817 4 1 391 0.030 0 3 35 6 16 12.5 2 2 753 95 13 3700.006 0 3 13 1 9 50 25 2 3 560 22 4 267 0.004 0 3 27 1 2 12.5 2 3 450 4811 217 0.028 0 3 17 3 18

TABLE 3 Erenna assay with PT 60154-4-IG as capture antibody and MABE230as detection antibody MPs Cap [SMN] DE LoD (μg/ Det Ab Ab/MP (pg/ DE CV(pg/ well) (ng/mL) (μg/mg) mL) n DE SD % Slope mL) 10 1000 25 10 3 3368173 5 329 0.034 0 2 74 6 8 12.5 10 3 3722 71 2 361 0.123 0 3 117 22 19500 25 10 3 2135 91 4 209 0.006 0 3 43 1 1 12.5 10 3 2175 203 9 2130.126 0 2 50 13 27 100 25 10 3 505 67 13 48 0.143 0 3 22 3 16 12.5 10 3523 46 9 51 0.140 0 2 17 4 21 50 25 10 3 269 30 11 25 0.368 0 3 24 5 1912.5 10 3 302 32 11 29 0.438 0 2 12 6 55 5 1000 25 10 3 3441 167 5 3390.083 0 3 48 14 29 12.5 10 3 3574 176 5 351 0.069 0 3 62 12 20 500 25 103 2044 149 7 202 0.045 0 3 24 5 19 12.5 10 3 1958 77 4 192 0.073 0 3 337 21 100 25 10 3 481 52 11 47 0.024 0 3 10 1 6 12.5 10 2 501 31 6 490.109 0 3 13 3 20 50 25 10 3 256 22 9 25 0.113 0 2 5 1 28 12.5 10 3 23124 10 23 0.250 0 2 5 3 57

Example 4: Generation of Standard Curve Using Recombinant SMN Proteinand Estimation of LLoQ

Based on the results presented in Example 2, MABE230 was used as thecapture antibody and PT60154-1-Ig was used as the detection antibody togenerate a standard curve and estimate the lower limit of quantitation(LLoQ) of the assay. The Erenna assay was run using the protocoldescribed in Example 2 except that fewer conditions were tested based onthe Example 2 results: MPs were mixed with 12.5 μg of MABE230 captureantibody per mg of MPs and diluted to 50 μg/mL in assay buffer; and thedetection antibody was diluted to 500, or 1,000 ng/mL in assay buffer.In order to generate the standard curve, 11 different concentrations ofHis-tagged recombinant human SMN protein in standard diluent (see Table4) plus a control containing only standard diluent (0 pg/mL) weretested.

In Table 4, “Det Ab” indicates detection antibody, “n” indicates thenumber of replicate runs completed, “DE” indicates average detectedevents for each set of replicates, “CV %” indicates the percentcoefficient of variation, “EP” indicates event photons, which is the sumof the photons counted in all of the detected events, and “ND” indicatesnot detected. The calculated SMN concentrations (“Calc [SMN]”) weredetermined using the Erenna system SMD algorithm and Sgx Link software(Singulex), which takes into account detected events, event photons, andtotal photons in order to calculate analyte concentration across a widedynamic range. “% recovery” is the percent of the calculated SMNconcentration relative to the concentration of SMN analyte used.

TABLE 4 Standard curves generated with recombinant human SMN DE EP CalcCalc % [SMN] CV CV [SMN] [SMN] Recov- (pg/mL) n DE % EP % (pg/mL) CV %ery 500 ng/mL Det Ab 200.00 3 9463 3 18559403 4 201.61 8 101 66.67 312028 3 9530749 3 66.56 2 100 22.22 3 12224 5 3847763 18 26.20 16 1187.41 3 5963 2 1047911 2 7.24 2 98 3.70 2 3190 0 496941 4 3.32 1 90 1.853 1846 15 267497 15 1.82 16 98 0.93 3 967 9 135432 9 0.93 9 101 0.46 3562 15 77541 15 0.53 16 115 0.23 3 301 4 39971 4 0.27 4 115 0.12 3 15413 19480 16 0.11 19 97 0.06 2 91 5 14178 19 0.083 72 144 0.00 3 33 265660 64 ND ND ND 1000 ng/mL Det Ab 200.00 3 9361 4 20380681 2 200.58 3100 66.67 3 11455 2 10594814 1 64.49 1 97 22.22 3 13136 1 4635858 924.68 9 111 7.41 3 7203 2 1320582 3 7.20 2 97 3.70 3 4327 5 706215 63.82 5 103 1.85 2 2137 3 312351 5 1.73 4 93 0.93 3 1170 7 170598 9 0.9611 104 0.46 3 630 11 87395 11 0.48 11 104 0.23 3 330 4 44780 5 0.24 5102 0.12 3 193 10 26294 10 0.12 14 104 0.06 3 125 19 15866 25 0.06 34105 0.00 3 56 33 6807 32 ND ND ND

The standard curves for the 500 ng/mL and 1000 ng/mL detection antibodydata sets were generated by plotting signal generated by the SMDalgorithm against SMN concentration for the samples that generated lessthan 1,000 detected events. The slope of the standard curve for the 500ng/mL detection antibody data set was 977, and the slope of the standardcurve for the 1000 ng/mL detection antibody data set was 1210.

The LLoQ was defined as the lowest point on the standard curve with acalculated SMN concentration with a % recovery within 80-120% and CV%≦20%. Based on those criteria, the LLoQ was 0.12 pg/mL for both datasets. Since the LLoQ was the same for both concentrations of detectionantibody tested, average CV %'s were also evaluated. Average CV % for DEwas approximately equal (8.4%) for both detection antibodyconcentrations, but the average CV % for EP was 14.4% for 500 ng/mLdetection antibody and 9.8% for 1000 ng/mL detection antibody. Due tothe lower average EP CV % and greater slope of the standard curve, 1000ng/mL detection antibody was used in subsequent experiments.

Example 5: Determination of the Lower Limit of Reliable Quantitation(LLoRQ)

The LLoQ of 0.12 pg/mL determined in Example 3 was verified byperforming the assay with various SMN protein levels below and above0.12 pg/mL. The Erenna assay was run using the general protocoldescribed in Example 2. Specifically, MPs were mixed with 12.5 μg ofMABE230 capture antibody per mg of MPs and diluted to 50 μg/mL in assaybuffer; and the detection antibody was diluted to 1,000 ng/mL in assaybuffer. The concentrations of SMN protein used are shown in Table 5below.

In Table 5, “n” indicates the number of replicates, “DE” indicatesaverage detected events, “SD” indicates standard deviation, and “CV %”indicates percent coefficient of variance. The calculated SMNconcentrations (“Calc [SMN]”) and % recovery were determined as inExample 3. The LLoRQ is defined as the analyte concentration at whichrecoveries are within 80-120% with less than 20 CV % for concentrationsgreater than one half of the LLoQ and recoveries are within 75-125% withless than 25 CV % for concentrations less than or equal to one half theLLoQ. The results in Table 5 show that the LLoQ of 0.12 pg/mL met theserequirements and was determined to be the LLoRQ.

TABLE 5 Determination of LLoRQ DE Calc Calc Calc Re- [SMN] DE CV [SMN][SMN] [SMN] cov- (pg/mL) n DE SD % (pg/mL) SD CV % ery 1.20 (10x 2 142947 3 1.16 0.0412 4 96 LLoQ) 0.60 (5x LLoQ) 3 763 22 3 0.62 0.0147 2 1030.24 (2x LLoQ) 3 362 26 7 0.27 0.0224 8 114 0.12 (1x LLoQ) 3 201 4 20.13 0.0035 3 109 0.06 (0.5x 2 138 18 13 0.07 0.0170 23 122 LLoQ)

Example 6: Prototype Sample Testing with Human Cerebral Spinal Fluid(CSF)

Prototype testing of the SMN assay with human CSF samples was completedusing the assay conditions described in Example 4. Five different humanCSF samples containing endogenous SMN protein were analyzed with andwithout spiked His-tagged recombinant human SMN protein at 5 or 10pg/mL. The results are shown in Table 6 below. See Example 4 for a listof the abbreviations found in Table 6. Each DE value shown is theaverage of two replicate samples. In Table 6, the % recovery wascalculated by subtracting the calculated endogenous SMN concentration ofthe unspiked sample from the calculated total SMN concentration(including endogenous and recombinant SMN) of the spiked sample,dividing that result by the known concentration of spiked recombinantSMN, and multiplying that result by 100. Thus, the % recovery valuesrefer only to the spiked, recombinant SMN protein and are not applicableto the unspiked samples that contain only endogenous SMN protein.

TABLE 6 Prototype testing of human CSF Human Calc % CSF [SMN] DE [SMN]Calc Calc Re- sample spiked DE CV (pg/ [SMN] [SMN] cov- No. (pg/mL) DESD % mL) SD CV % ery 1 0.0 330 1 0 0.28 0.00 0 n/a 5.0 5072 389 8 5.100.47 9 96 10.0 9733 385 4 13.18 1.35 10 129 2 0.0 240 49 20 0.20 0.04 23n/a 5.0 5312 7 0 5.39 0.02 0 104 10.0 9626 47 0 12.86 0.12 1 127 3 0.0278 13 5 0.23 0.01 5 n/a 5.0 5982 110 2 6.27 0.09 1 121 10.0 9141 420 511.92 0.76 6 117 4 0.0 375 48 13 0.32 0.04 13 n/a 5.0 5812 34 1 6.100.11 2 116 10.0 8655 444 5 10.81 0.73 7 105 5 0.0 479 15 3 0.41 0.01 3n/a 5.0 6074 322 5 6.46 0.43 7 121 10.0 9437 66 1 12.32 0.11 1 119

Example 7: Testing of Various Salt and Surfactant Concentrations

In order to evaluate assay performance in various salt and surfactantconcentrations, recombinant human SMN was analyzed with 150, 450, 600,or 700 mM sodium chloride and 0.1, 0.25, 0.5, or 1% Triton-X detergentin the assay buffer using the protocol described in Example 4. Theresults are shown in Table 7, and the table abbreviations are listed inExample 4.

TABLE 7 Assay result with various salt and surfactant concentrations[Sur- [SMN] DE LOD [NaCl] factant] (pg/ DE CV (pg/ (mM) (%) mL) n DE SD% slope mL) 150 0.1 2 3 2104 254 12 1020 0.019 0 3 65 10 15 0.25 2 32411 165 7 1177 0.017 0 2 57 10 17 0.5 2 3 2565 252 10 1244 0.026 0 3 7716 21 1 2 3 2211 231 10 1057 0.046 0 3 96 25 25 450 0.1 2 3 1546 139 9744 0.009 0 3 59 3 5 0.25 2 2 2068 8 0 1003 0.003 0 2 61 1 2 0.5 2 31891 59 3 916 0.012 0 3 60 5 9 1 2 3 1501 268 18 715 0.022 0 2 72 8 11600 0.1 2 3 1075 103 10 516 0.004 0 3 44 1 2 0.25 2 3 1170 73 6 5620.011 0 3 46 3 7 0.5 2 3 1115 101 9 525 0.069 0 3 66 18 27 1 2 3 1064136 13 501 0.016 0 3 62 4 6 700 0.1 2 3 749 117 16 351 0.012 0 3 48 2 40.25 2 3 766 80 10 360 0.016 0 2 47 3 6 0.5 2 2 817 21 3 379 0.004 0 259 1 1 1 2 2 711 70 10 326 0.080 0 3 59 13 22

In order to maximize assay performance, the highest salt and surfactantconcentrations that were not detrimental to assay performance wereselected. High salt and surfactant concentrations decrease backgroundand non-specific binding but can also cause reductions in slope, loss ofassay sensitivity, and increase in LoD (Lower Limit of Detection). Thus,150 mM salt and 0.25% surfactant were chosen or subsequent experiments,because those conditions achieved a high slope, low LoD, and lowbackground (low detected events at 0 pg/mL SMN).

Example 8: Generation of Standard Curve and Verification of LLoQ

Based on the results presented in Example 6, 150 mM salt and 0.25%surfactant were used in the assay buffer to generate a standard curveand verify the lower limit of quantitation (LLoQ) of the assay. TheErenna assay was run using the protocol described in Example 4. In orderto generate the standard curve, 11 different concentrations ofHis-tagged recombinant human SMN protein in standard diluent (see Table8) plus a standard diluent only (0 pg/mL) control were tested.

In Table 8, “n” indicates the number of replicate runs completed, “DE”indicates average detected events for each set of replicates, “CV %”indicates the percent coefficient of variation, and “ND” indicates notdetected. The calculated SMN concentrations and % recovery weredetermined as in Example 3.

TABLE 8 Standard curve generated with recombinant human SMN DE Calc CalcCalc % [SMN] DE CV [SMN] [SMN] [SMN] Recov- (pg/mL) n DE SD % (pg/mL) SDCV % ery 100.00 2 ND ND ND 98.79 3.26 3 99 33.33 3 ND ND ND 33.98 1.31 4102 11.11 3 ND ND ND 11.76 0.54 5 106 3.70 3 ND ND ND 3.72 0.18 5 1001.85 2 ND ND ND 1.94 0.25 13 105 0.93 3 1015 115 11 0.82 0.10 12 89 0.462 605 20 3 0.48 0.02 3 104 0.23 3 314 31 10 0.24 0.03 11 103 0.12 2 1904 2 0.13 0.00 2 112 0.06 3 111 6 5 0.06 0.01 9 100 0.03 3 74 4 5 0.020.00 16 82 0.00 2 50 1 3 0.01 ND ND ND

The standard curve was generated as in Example 3, using the data inTable 8. The slope of the standard curve was 1062, and the LLoQ was 0.03pg/mL.

Example 9: Determination of Spike Recovery and Linearity of Dilution inHuman CSF

The Erenna assay was performed as described in Example 7. Eightdifferent human CSF samples were spiked with 0 or 1.2 pg/mL His-taggedrecombinant human SMN protein, then analyzed to determine the % recoveryof the spiked SMN protein, as in Example 5. Dilutions of the human CSFspiked with 1.2 pg/mL were then made and analyzed in order to determinethe linearity of the assay. The experiment was repeated with varioussamples on separate days, and the results of both experiments are shownin Tables 9 and 10.

See Example 4 for a list of the abbreviations found in Tables 9 and 10.The % recovery was calculated as in Example 5. The % linearity of eachdilution was determined by multiplying the calculated SMN concentrationby two, then determining the percent of that result relative to thecalculated SMN concentration corresponding to the dilution that wastwice as concentrated.

TABLE 9 Spike recovery and linearity of dilution in human CSF Human CSFsample No. + Calc % piked DE [SMN] Calc Calc Re- % SMN or DE CV (pg/[SMN] [SMN] cov- Line- dilution n DE SD % mL) SD CV % ery arity 2 + 1.23 1346 114 8 1.36 0.12 8 97 n/a pg/mL 1:2 dilution 3 651 29 4 0.66 0.035 n/a 97 1:4 dilution 3 305 42 14 0.29 0.05 16 n/a 89 1:8 dilution 3 18514 7 0.15 0.02 11 n/a 106 2 + 0 pg/mL 2 222 20 9 0.20 0.02 12 n/a n/a3 + 1.2 3 1456 53 4 1.47 0.05 4 87 n/a pg/mL 1:2 dilution 3 714 110 150.72 0.11 15 n/a 98 1:4 dilution 3 361 57 16 0.35 0.06 17 n/a 98 1:8dilution 3 216 29 14 0.19 0.03 18 n/a 108 3 + 0 pg/mL 3 434 12 3 0.430.01 3 n/a n/a 4 + 1.2 2 1251 21 2 1.27 0.02 2 85 n/a pg/mL 1:2 dilution2 692 28 4 0.70 0.03 4 n/a 111 1:4 dilution 2 380 24 6 0.38 0.03 7 n/a107 1:8 dilution 2 186 27 14 0.16 0.03 21 n/a 83 4 + 0 pg/mL 2 267 49 190.25 0.06 23 n/a n/a 5 + 1.2 2 1571 7 0 1.59 0.01 0 99 n/a pg/mL 1:2dilution 2 788 14 2 0.80 0.01 2 n/a 101 1:4 dilution 2 341 28 8 0.330.03 9 n/a 83 1:8 dilution 2 206 6 3 0.23 0.07 33 n/a 136 5 + 0 pg/mL 1398 n/a n/a 0.40 n/a n/a n/a n/a 6 + 1.2 2 1433 170 12 1.45 0.18 12 94n/a pg/mL 1:2 dilution 2 682 90 13 0.69 0.09 13 n/a 95 1:4 dilution 2348 6 2 0.34 0.01 2 n/a 98 1:8 dilution 2 194 27 14 0.17 0.03 19 n/a 976 + 0 pg/mL 1 336 n/a n/a 0.33 n/a n/a n/a n/a

TABLE 10 Spike recovery and linearity of dilution in human CSF Human CSFsample No. + Calc % spiked DE [SMN] Calc Calc Re- % SMN or DE CV (pg/[SMN] [SMN] cov- Line- dilution n DE SD % mL) SD CV % ery arity 2 + 1.23 1669 97 6 1.55 0.10 6 115 n/a pg/mL 1:2 dilution 3 767 41 5 0.67 0.046 n/a 86 1:4 dilution 3 369 10 3 0.30 0.01 3 n/a 91 1:8 dilution 3 214 84 0.16 0.01 4 n/a 105 2 + 0 pg/mL 3 230 17 7 0.17 0.02 9 n/a n/a 3 + 1.23 1709 160 9 1.59 0.17 10 99 n/a pg/mL 1:2 dilution 3 769 31 4 0.67 0.034 n/a 84 1:4 dilution 3 406 11 3 0.34 0.01 3 n/a 100 1:8 dilution 3 24220 8 0.19 0.02 10 n/a 110 3 + 0 pg/mL 3 469 44 9 0.40 0.04 10 n/a n/a7 + 1.2 2 2078 50 2 1.98 0.06 3 77 n/a pg/mL 1:2 dilution 2 1005 134 130.89 0.13 14 n/a 90 1:4 dilution 2 398 5 1 0.33 0.00 1 n/a 74 1:8dilution 2 254 26 10 0.20 0.02 12 n/a 119 7 + 0 pg/mL 2 1174 41 3 1.060.04 3 n/a n/a 1 + 1.2 2 1475 9 1 1.35 0.01 1 92 n/a pg/mL 1:2 dilution2 713 6 1 0.62 0.01 1 n/a 92 1:4 dilution 2 400 21 5 0.33 0.02 6 n/a 1071:8 dilution 2 219 7 3 0.16 0.01 4 n/a 99 1 + 0 pg/mL 2 306 38 12 0.250.04 15 n/a n/a 8 + 1.2 2 2554 54 2 2.51 0.06 2 120 n/a pg/mL 1:2dilution 2 1060 69 6 0.94 0.07 7 n/a 75 1:4 dilution 2 552 70 13 0.470.06 14 n/a 100 1:8 dilution 2 232 67 29 0.18 0.06 36 n/a 74 8 + 0 pg/mL2 1190 91 8 1.07 0.09 8 n/a n/a

Example 10: Determination of Intra-Assay and Inter-Assay Precision withHuman CSF

In order to evaluate intra-assay precision, five human CSF samples werespiked with 0.6 pg/mL recombinant SMN protein, and six replicates ofeach sample were analyzed using the Erenna assay as described in Example7. The results are shown in Table 11.

In order to evaluate inter-assay precision, the results from samplenumbers 2 and 3 and their respective dilutions, shown in Tables 9 and 10in Example 8 were analyzed. The results shown in Table 12 are thecombined results for the two replicate experiments, which were performedon separate days.

In Table 11, “R” indicates a replicate, and other abbreviations inTables 11 and 12 are listed in Example 4.

TABLE 11 Intra-assay precision with human CSF Detected Events (DE) HumanCSF sample No. + spiked CV SMN R1 R2 R3 R4 R5 R6 Mean SD % 2 + 0.6 14261351 1272 1080 1263 1341 1289 118 9 pg/mL 3 + 0.6 1737 1458 1699 15671689 1786 1656 121 7 pg/mL 4 + 0.6 1377 1389 1411 1396 1348 1423 1391 262 pg/mL 5 + 0.6 1544 1618 1552 1640 1663 1812 1638 98 6 pg/mL 6 + 0.61545 1539 1498 1557 1377 1513 1505 66 4 pg/mL Calc [SMN] (pg/mL) HumanCSF sample No. + spiked CV SMN R1 R2 R3 R4 R5 R6 Mean SD % 2 + 0.6 0.870.83 0.78 0.66 0.77 0.82 0.79 0.07 9 pg/mL 3 + 0.6 1.07 0.90 1.04 0.961.04 1.10 10.2 0.07 7 pg/mL 4 + 0.6 0.85 0.85 0.86 0.91 0.83 0.87 0.860.03 3 pg/mL 5 + 0.6 0.95 0.99 0.95 1.01 1.02 1.11 1.00 0.06 6 pg/mL 6 +0.6 0.95 0.94 0.92 0.96 0.85 0.93 0.92 0.04 4 pg/mL

TABLE 12 Inter-assay precision with human CSF based on data shown inTables 9 and 10 Human CSF sample No. + spiked SMN Calc [SMN] Calc [SMN]Calc [SMN] or dilution (pg/mL) SD CV % 2 + 1.2 pg/mL 1.46 0.13 9 1:20.67 0.01 1 1:4 0.30 0.01 3 1:8 0.16 0.00 2  2 + 0 pg/mL 0.19 0.02 9 3 +1.2 pg/mL 1.53 0.08 5 1:2 0.70 0.04 5 1:4 0.35 0.01 4 1:8 0.19 0.00 2 3 + 0 pg/mL 0.41 0.03 7

Example 11: Transgenic Mouse CSF Testing

CSF from eleven transgenic mice expressing human SMN1 was collected andpooled into four samples, then diluted with standard diluent in orderfor all samples to contain the same total volume. The concentration ofhuman SMN protein in each sample was determined by performing the Erennaassay as described in Example 7. The results are shown in Table 13, andthe abbreviations in Table 13 are listed in Example 4.

TABLE 13 Concentration of human SMN in transgenic mouse CSF Dilution DECalc Calc Calc corrected Sam- DE CV [SMN] [SMN] [SMN] Dilution [SMN] plen DE SD % (pg/mL) SD CV % factor (pg/mL) 1 2 1517 30 2 1.45 0.03 2.3 9.814.2 2 2 970 57 6 0.88 0.06 6.5 8.0 7.0 3 2 3061 2 0 3.35 0.01 0.3 14.147.2 4 2 1000 59 6 0.91 0.06 6.8 8.1 7.4

Example 12: Human CSF Testing

The concentration of SMN protein in fifty-five undiluted human CSFsamples was determined using the Erenna assay as described in Example 7.The results are shown in Table 14, and the abbreviations in Table 14 arelisted in Example 4. Sample 28 produced an abnormally high value,possibly due to contamination with blood, and the sample was hemolyzed.

TABLE 14 Concentration of SMN human CSF Calc Calc Calc [SMN] Sam- DE DE[SMN] [SMN] CV ple n DE SD CV % (pg/mL) SD % 9 2 343 8 2 0.26 0.01 3 102 575 47 8 0.47 0.04 9 11 2 671 51 8 0.56 0.05 8 12 2 970 117 12 0.830.11 13 13 2 343 11 3 0.26 0.01 4 14 2 538 18 3 0.44 0.01 3 15 2 950 232 0.81 0.02 3 16 2 776 24 3 0.65 0.02 3 17 2 551 52 9 0.45 0.05 10 18 2373 16 4 0.28 0.01 5 19 2 1509 99 7 1.31 0.09 7 20 2 590 54 9 0.49 0.049 21 2 378 12 3 0.29 0.01 4 22 2 1357 53 4 1.18 0.05 4 23 2 1066 8 10.92 0.02 2 24 2 503 43 9 0.40 0.04 10 25 2 579 55 10 0.48 0.05 11 26 2356 11 3 0.27 0.01 4 27 2 493 1 0 0.40 0.00 1 28 1 10974 n/a n/a 16.97n/a n/a 29 2 783 90 11 0.57 0.07 12 30 2 823 1 0 0.70 0.00 0.1 31 2 68055 8 0.49 0.05 10 32 1 386 n/a n/a 0.26 n/a n/a 33 2 686 8 1 0.57 0.01 134 2 506 45 9 0.41 0.04 10 35 2 861 64 7 0.63 0.05 8 36 2 572 47 8 0.470.04 9 37 2 398 77 19 0.27 0.06 22 38 2 656 121 18 0.47 0.09 20 39 2 69099 14 0.50 0.08 16 40 2 472 22 5 0.33 0.02 5 41 2 524 52 10 0.37 0.04 1142 2 1102 61 6 0.82 0.05 6 43 2 544 66 12 0.39 0.05 13 44 2 865 63 70.63 0.05 8 45 2 1127 77 7 0.85 0.06 7 46 2 338 18 5 0.23 0.01 6 47 2428 34 8 0.30 0.03 9 48 2 630 37 6 0.45 0.03 6 49 2 1447 3 0 1.12 0.000.1 50 2 328 35 11 0.22 0.03 12 51 1 223 n/a n/a 0.14 n/a n/a 52 2 58681 14 0.42 0.06 15 53 2 328 42 13 0.22 0.03 14 54 2 795 66 8 0.58 0.05 955 2 403 21 5 0.28 0.02 6 56 2 234 4 2 0.15 0.00 2 57 2 615 59 10 0.440.04 10 58 2 531 7 1 0.38 0.01 1 59 2 432 21 5 0.30 0.02 5 60 2 1109 434 0.83 0.03 4 61 2 1232 44 4 0.93 0.04 4 62 2 571 52 9 0.40 0.04 10 63 2544 35 6 0.39 0.03 7

As determined in the above examples, the assay parameters met specifiedthresholds. The LoD was well below the target of 0.1 pg/mL SMN protein(see Examples 2 and 6), the LLoQ and LLoRQ of 0.12 pg/mL (see Examples 3and 4) was sufficient to detect endogenous SMN protein levels in humanCSF (see Examples 5, 8, and 11). The average intra-assay precision of3-9% CV and average inter-assay precision of 1-9% CV were well withinthe target limit of 20% CV (see Example 9). The percent recovery ofspiked recombinant human SMN protein (see Examples 3, 4, 5, 7, and 8)and the % linearity of sample dilutions (see Example 8) were within80-12% for at least 80% of samples tested.

Example 13: Single Administration Study of ISIS 396443

A single dose of ISIS 396443 was administered intrathecally as a lumbarpuncture bolus injection using a spinal anesthesia needle between 21gauge and 25 gauge. Before patients received a dose of ISIS 396443, asample of CSF was taken and the amount of SMN protein present in thesample was measured and used as the baseline concentration of SMNprotein in the CSF. Additionally, before patients received a dose ofISIS 396443, each patient was evaluated according to the HammersmithMotor Function Scale-Expanded (HFMSE), and this HFMSE score was used aseach patient's baseline HFMSE score.

Between 9 and 14 months after each patient received a dose of ISIS396443, samples of CSF were taken and the amount of SMN protein presentin the sample was measured. The amount of SMN protein measured between 9and 14 months was then compared to the baseline concentration of SMNprotein measured before therapy commenced and these values are presentedin Table 15 below under the “% increase from baseline SMN protein”heading. The percentage amounts given under the “% increase frombaseline SMN protein” heading indicate the percent increase in theamount of SMN protein compared to baseline. Additionally, between 9 and14 months after each patient received a dose of ISIS 396443, eachpatient was evaluated according to the Hammersmith Motor FunctionScale-Expanded (HFMSE). The average change in HFMSE for all patients ina patient group relative to the baseline HFMSE measurement is presentedin Table 15 below under the “Change in HFMSE at 9-14 months” heading.

Table 15 below illustrates that an increase in the amount of SMN proteinpresent in the CSF was associated with a clinical improvement insubjects, as measured by an increase in Hammersmith motor scores. Forexample, patients in group 3, who received a 6 mg dose of ISIS 396443had an average change in HFMSE of +2.5 and an increase in SMN proteinrelative to the baseline. Similarly, patients in group 4, who received a9 mg dose of ISIS 396443 had an average change in HFMSE of +5.75 and aneven greater increase in SMN protein relative to the baseline comparedto patients in the 1 mg, 3 mg, and 6 mg group.

TABLE 15 Single Administration Study of ISIS 396443 Change in % increasefrom Patient # Dose HFMSE at 9-14 baseline SMN Group Patients (mg)months protein 1 6 1 −1.7  62% 2 6 3 +0.5  38% 3 6 6 +2.5 118% 4 10 9+5.75 160%

Example 14: Multiple Dose Administration Study of ISIS 396443

In a Phase 1/2a multiple dose study involving 25 patients having SMA,patient therapy was commenced. Before patients received a dose of ISIS396443, a sample of CSF was taken and the amount of SMN protein presentin the sample was measured and used as the baseline concentration of SMNprotein in the CSF. Additionally, before patients received a dose ofISIS 396443, each patient was evaluated according to the HammersmithMotor Function Scale-Expanded (HFMSE), and this HFMSE score was used aseach patient's baseline HFMSE score.

ISIS 396443 was administered intrathecally as a lumbar puncture bolusinjection using a spinal anesthesia needle between 21 gauge and 25gauge. The dose amounts, number of patients receiving each dose, anddose frequency for multiple doses are listed in the table below.Patients having SMA and receiving a dose of 3 mg or 6 mg received asecond dose approximately 29 days after the first dose and received athird dose approximately 85 days after receiving the first dose.Patients having SMA and receiving a dose of 9 mg received a second doseof ISIS 396443 approximately 85 days after receiving a first dose. Inthe table below “ND” stands for no dose. For example, SMA patients thatreceive a dose of 9 mg of ISIS 396443 on day 1 receive a second 9 mgdose of ISIS 396443 on day 85 and no dose of ISIS 396443 on day 29.Proposed dose frequency is approximate, for example, if the dosefrequency is a dose at day 1 and a second dose at day 29, an SMA patientmay receive a second dose 25, 26, 27, 28, 29, 30, 31, 32, 33, or 34 daysafter receipt of the first dose.

A sample of CSF was collected from each patient during each subsequentdose. For example, if a patient were to receive a dose of ISIS 396443 atday 1, day 29, and day 85, a sample of CSF for analysis would becollected from the patient at day 1, day 29, and day 85. Additionally,each patient was evaluated according to the Hammersmith Motor FunctionScale-Expanded (HFMSE) at day 1, day 29, and day 85, and 9 months outfrom their first dose.

TABLE 16 Multiple Dose Administration Study of ISIS 396443 Patient #Dose at Day 1 Dose at Day 29 Dose at Day 85 Group Patients (mg) (mg)(mg) 1 8 3 3 3 2 8 6 6 6 3 9 9 ND 9

At 3 months after each patient received their first dose of ISIS 396443,samples of CSF were taken and the amount of SMN protein present in thesample was measured. The average % of SMN protein in the CSF relative tothe baseline SMN protein in the CSF (measured before SMA patientsreceived the first dose of ISIS 396443) was analyzed for all patients ineach patient group. The average % increase of SMN protein in the CSFrelative to the baseline SMN protein in the CSF is presented in Table 17below under the “% increase from baseline SMN protein” heading. Thepercentage amounts given under the “% increase from baseline SMNprotein” heading indicate the percent increase in the amount of SMNprotein compared to baseline. Nine (9) months after each patientreceived a dose of ISIS 396443, each patient was evaluated according tothe Hammersmith Motor Function Scale-Expanded (HFMSE). The averagechange in HFMSE for all patients in a patient group is presented inTable 17 below under the “Change in HFMSE at 9-14 months” heading. Table15 below illustrates that an increase in the amount of SMN proteinpresent in the CSF was associated with a clinical improvement insubjects, as measured by an increase in Hammersmith motor scores.

TABLE 17 Multiple Dose Administration Study of ISIS 396443 Change in %increase from Patient # Dose HFMSE at 9 baseline SMN Group Patients (mg)months protein 1 8 3 +1.5 23% 2 8 6 +2.3 15% 3 9 9 +3.7 114% 

This example shows consistent dose-dependent and time-dependentimprovements in a motor function outcome relevant for SMA and acorrelated increase in the amount of SMN protein in the CSF.

1. A method of determining the amount of SMN protein in a biologicalsample comprising: a. collecting a biological sample from a humansubject; b. contacting the biological sample with a capture antibody; c.contacting the biological sample with a detection antibody; d. measuringthe amount of detection antibody in the biological sample; andcalculating the amount of SMN protein in the biological sample.
 2. Themethod of claim 1, wherein the biological sample is cerebrospinal fluid.3. The method of claim 1, wherein the biological sample is contactedwith the capture antibody before it is contacted with the detectionantibody.
 4. (canceled)
 5. (canceled)
 6. The method of claim 1, whereinthe capture antibody recognizes an N-terminal epitope of the SMN2protein.
 7. The method of claim 1, wherein the capture antibodyspecifically binds to a polypeptide sequence comprising SEQ ID NO: 25 orSEQ ID NO:
 26. 8. (canceled)
 9. (canceled)
 10. The method of claim 1,wherein the capture antibody is Millipore antibody MABE230.
 11. Themethod of claim 1, wherein the detection antibody specifically binds tothe polypeptide of SEQ ID NO: 27 or SEQ ID NO:28.
 12. (canceled) 13.(canceled)
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 26. (canceled)27. (canceled)
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 29. The method of claim 1, wherein thesubject has spinal muscular atrophy (SMA).
 30. The method of claim 29,wherein the subject has type I SMA, typ II SMA, type III SMA, or type IVSMA.
 31. (canceled)
 32. (canceled)
 33. (canceled)
 34. The method ofclaim 1, wherein the subject has received at least one dose of apharmaceutical agent for the treatment of SMA.
 35. The method of claim34, wherein the pharmaceutical agent for the treatment of SMA is anantisense compound that is ISIS396443.
 36. (canceled)
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 59. A method of treating ahuman subject having SMA comprising: a. detecting the amount of SMNprotein in a sample of cerebrospinal fluid according to the method ofclaim 1; and b. administering a second or more doses of ISIS
 396443. 60.A method of determining the dosing frequency of ISIS 396443 comprising:a. administering a first dose of ISIS 396443 to a human subject in needthereof; b. detecting the amount of SMN protein in a sample ofcerebrospinal fluid according to the method of any of claim 1 at thetime a second dose is administered; and c. increasing or decreasing thefrequency of any subsequent doses of ISIS
 396443. 61. A method ofdetermining the dosing frequency of ISIS 396443 comprising: a.administering a first dose of ISIS 396443 to a human subject in needthereof; b. detecting the amount of SMN protein in a sample ofcerebrospinal fluid according to the method of claim 1 at the time thefirst dose is administered; c. detecting the amount of SMN protein in asample of cerebrospinal fluid according to the method of claim 1 at thetime the second dose is administered; and d. increasing or decreasingthe frequency of any subsequent doses of ISIS
 396443. 62. The method ofclaim 60, wherein (i the frequency of the subsequent dose is increased;or (ii) the frequency of the subsequent dose is decreased. 63.(canceled)
 64. The method of claim 60, wherein the second dose isadministered (i) between 12 and 18 days after the first dose; (ii)between 24 and 34 days after the first dose; (iii) between 80-90 daysafter the first dose; (iv) 12-18 days after the first dose, and whereina subsequent dose is administered 25-35 days after the first dose; (v)12-18 days after the first dose, and wherein a subsequent dose isadministered 80-90 days after the first dose; (vi) 25-35 days after thefirst dose, a third dose is administered 80-90 days after the firstdose, and a fourth dose is administered 270-280 days after the firstdose; (vii) 25-35 days after the first dose, a third dose isadministered 80-90 days after the first dose, a fourth dose isadministered 270-280 days after the first dose, and each subsequent dosethereafter is administered at six month intervals; (viii) 12-18 daysafter the first dose, a third dose is administered 25-35 days after thefirst dose, a fourth dose is administered 60-70 days after the firstdose, a fifth dose is administered 178-188 days after the first dose,and a sixth dose is administered 298-308 days after the first dose isadministered; (ix) 12-18 days after the first dose, a third dose isadministered 25-35 days after the first dose, a fourth dose isadministered 60-70 days after the first dose, a fifth dose isadministered 178-188 days after the first dose, a sixth dose isadministered 298-308 days after the first dose is administered, and eachsubsequent dose thereafter is administered at four month intervals. 65.(canceled)
 66. (canceled)
 67. (canceled)
 68. (canceled)
 69. (canceled)70. (canceled)
 71. (canceled)
 72. (canceled)
 73. The method of claim 59,wherein the amount of SMN protein detected at the time the second doseis administered is at least 50% greater, 60% greater, 70% greater, 80%greater, 90% greater, 100% greater, 110% greater, 120% greater, 150%greater, or 200% greater than the amount of SMN protein detected at thetime the first dose was administered.
 74. (canceled)
 75. (canceled) 76.(canceled)
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 80. (canceled)81. (canceled)
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 89. (canceled)90. (canceled)
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 98. (canceled)99. (canceled)
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 102. (canceled) 103.(canceled)
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 110. (canceled) 111.(canceled)
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 126. (canceled)
 127. A kitfor detecting the amount of SMN protein in a sample of cerebrospinalfluid comprising: a. a capture antibody labeled with a magneticmicroparticle; b. a detection antibody labeled with a fluorophore. 128.(canceled)
 129. A kit for detecting the amount of SMN protein in asample of cerebrospinal fluid comprising: a. a capture antibody labeledwith a magnetic microparticle configured to bind with high specificityto an SMN protein; b. a detection antibody labeled with a fluorophoreconfigured to bind with high specificity to an SMN protein; c. a deviceconfigured to detect the detection antibody labeled with a fluorophoreand to calculate the concentration of SMN protein in the sample ofcerebrospinal fluid.
 130. The kit of claim 127, wherein the captureantibody is Millipore antibody MABE230.
 131. The kit of claim 127,wherein the detection antibody is ProteinTech antibody #60154-1-Ig. 132.A method for treating a human subject having one or more symptomsassociated with spinal muscular atrophy (SMA), the method comprisingadministering by intrathecal injection doses of an antisense compoundcomprising an antisense oligonucleotide consisting of 18 linkednucleosides, wherein the oligonucleotide has a nucleobase sequenceconsisting of the nucleobase sequence SEQ ID NO: 1, wherein eachinternucleoside linkage of the oligonucleotide is a phosphorothioatelinkage, wherein each nucleoside of the oligonucleotide is a 2′-MOEnucleoside, and wherein each cytosine of the oligonucleotide is a5-methyl cytosine, wherein the doses comprise: (i) a first dose of 12 mgof the antisense compound; (ii) a second dose of 12 mg of the antisensecompound 12-18 days after administration of the first dose; (iii) athird dose of 12 mg of the antisense compound 25-35 days afteradministration of the first dose; (iv) a fourth dose of 12 mg of theantisense compound 60-70 days after administration of the first dose;and (v) a fifth dose of 12 mg of the antisense compound 178-188 daysafter administration of the first dose.
 133. The method of claim 132,wherein the administration to the human subject comprises: (i) a firstdose of 12 mg of the antisense compound; (ii) a second dose of 12 mg ofthe antisense compound approximately 15 days after administration of thefirst dose; (iii) a third dose of 12 mg of the antisense compoundapproximately 29 days after administration of the first dose; (iv) afourth dose of 12 mg of the antisense compound approximately 64 daysafter administration of the first dose; and (v) a fifth dose of 12 mg ofthe antisense compound approximately 183 days after administration ofthe first dose.
 134. The method of claim 132, wherein the subject isfurther administered at least one maintenance dose of the antisensecompound.
 135. The method of claim 132, wherein the human subject isadministered by intrathecal bolus injection.
 136. The method of claim132, wherein the human subject has (i) type I SMA; (ii) type II SMA;(iii) type III SMA; or (iv) type IV SMA.
 137. The method of claim 132,wherein the human subject is administered the antisense compound whenthe subject is: (i) between 1 and 15 years of age; (ii) less than oneweek old; (iii) less than one month old; (iv) less than 3 months old;(v) less than 6 months old; (vi) less than one year of age; (vii) lessthan 2 years of age; or (viii) older than 15 years of age.
 138. Themethod of claim 132, wherein the human subject is administered theantisense compound using a spinal anesthesia needle.
 139. The method ofclaim 132, wherein the antisense compound is administered at aconcentration of 2.4 mg/mL.
 140. The method of claim 132, wherein theantisense compound is administered in an injection volume of 5.0 mL.